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TypeError in test_atacseq #3225

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hackdna opened this issue May 18, 2020 · 0 comments
Closed

TypeError in test_atacseq #3225

hackdna opened this issue May 18, 2020 · 0 comments

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@hackdna
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hackdna commented May 18, 2020

Version info

  • bcbio version (bcbio_nextgen.py --version): 1.2.3
  • OS name and version: Ubuntu 18.04

To Reproduce

  • Exact bcbio command you have used:
    pytest tests/integration/test_automated_analysis.py::test_atacseq
  • Your sample configuration file: run_info-atacseq.yaml

Observed behavior

FAILED tests/integration/test_automated_analysis.py::test_atacseq - subprocess.CalledProcessError: Command '['bcbio_nextgen.py', '/tmp/bcbio/test_automated_output/bcbio_system.yaml', '/vagrant/tests/da...

Expected behavior
No failure

Log files

install_test_files = None, data_dir = '/vagrant/tests/data/automated'

    @pytest.mark.atacseq
    def test_atacseq(install_test_files, data_dir):
        """
        Test ATAC-seq pipeline
        """
        with make_workdir() as workdir:
            cl = ["bcbio_nextgen.py",
                  get_post_process_yaml(data_dir, workdir),
                  os.path.join(data_dir, os.pardir, "test_atacseq"),
                  os.path.join(data_dir, "run_info-atacseq.yaml")]
>           subprocess.check_call(cl)

tests/integration/test_automated_analysis.py:202:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

popenargs = (['bcbio_nextgen.py', '/tmp/bcbio/test_automated_output/bcbio_system.yaml', '/vagrant/tests/data/automated/../test_atacseq', '/vagrant/tests/data/automated/run_info-atacseq.yaml'],)
kwargs = {}, retcode = 1
cmd = ['bcbio_nextgen.py', '/tmp/bcbio/test_automated_output/bcbio_system.yaml', '/vagrant/tests/data/automated/../test_atacseq', '/vagrant/tests/data/automated/run_info-atacseq.yaml']

    def check_call(*popenargs, **kwargs):
        """Run command with arguments.  Wait for command to complete.  If
        the exit code was zero then return, otherwise raise
        CalledProcessError.  The CalledProcessError object will have the
        return code in the returncode attribute.

        The arguments are the same as for the call function.  Example:

        check_call(["ls", "-l"])
        """
        retcode = call(*popenargs, **kwargs)
        if retcode:
            cmd = kwargs.get("args")
            if cmd is None:
                cmd = popenargs[0]
>           raise CalledProcessError(retcode, cmd)
E           subprocess.CalledProcessError: Command '['bcbio_nextgen.py', '/tmp/bcbio/test_automated_output/bcbio_system.yaml', '/vagrant/tests/data/automated/../test_atacseq', '/vagrant/tests/data/automated/run_info-atacseq.yaml']' returned non-zero exit status 1.

/home/vagrant/local/share/bcbio/anaconda/lib/python3.6/subprocess.py:311: CalledProcessError
------------------------------------------------------------------------------------------- Captured stdout call -------------------------------------------------------------------------------------------
Running bcbio version: 1.2.3
global config: /tmp/bcbio/test_automated_output/bcbio_system.yaml
flowcell directory: /vagrant/tests/data/test_atacseq
run info config: /vagrant/tests/data/automated/run_info-atacseq.yaml
------------------------------------------------------------------------------------------- Captured stderr call -------------------------------------------------------------------------------------------
[2020-05-18T14:32Z] System YAML configuration: /tmp/bcbio/test_automated_output/bcbio_system.yaml.
[2020-05-18T14:32Z] Locale set to C.UTF-8.
[2020-05-18T14:32Z] Resource requests: bwa, picard; memory: 3.00, 3.00; cores: 16, 16
[2020-05-18T14:32Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job
[2020-05-18T14:32Z] Timing: organize samples
[2020-05-18T14:32Z] multiprocessing: organize_samples
[2020-05-18T14:32Z] Using input YAML configuration: /vagrant/tests/data/automated/run_info-atacseq.yaml
[2020-05-18T14:32Z] Checking sample YAML configuration: /vagrant/tests/data/automated/run_info-atacseq.yaml
[2020-05-18T14:32Z] Retreiving program versions from /home/vagrant/local/share/bcbio/manifest/python-packages.yaml.
[2020-05-18T14:32Z] Retreiving program versions from /home/vagrant/local/share/bcbio/manifest/r-packages.yaml.
[2020-05-18T14:32Z] Testing minimum versions of installed programs
[2020-05-18T14:32Z] Timing: alignment
[2020-05-18T14:32Z] multiprocessing: prepare_sample
[2020-05-18T14:32Z] Preparing Test1
[2020-05-18T14:32Z] gzipping /tmp/bcbio/data/atac/atac_1.fq to /tmp/bcbio/test_automated_output/fastq/atac_1.fq.gz.
[2020-05-18T14:32Z] gzipping /tmp/bcbio/data/atac/atac_2.fq to /tmp/bcbio/test_automated_output/fastq/atac_2.fq.gz.
[2020-05-18T14:32Z] multiprocessing: trim_sample
[2020-05-18T14:32Z] Skipping trimming of Test1.
[2020-05-18T14:32Z] multiprocessing: disambiguate_split
[2020-05-18T14:32Z] multiprocessing: process_alignment
[2020-05-18T14:32Z] Aligning lane Test1 with bwa aligner
[2020-05-18T14:32Z] bwa mem alignment from fastq: Test1
[2020-05-18T14:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2020-05-18T14:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2020-05-18T14:32Z] [M::mem_pestat] (25, 50, 75) percentile: (153, 292, 478)
[2020-05-18T14:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1128)
[2020-05-18T14:32Z] [M::mem_pestat] mean and std.dev: (328.82, 206.54)
[2020-05-18T14:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 1453)
[2020-05-18T14:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2020-05-18T14:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2020-05-18T14:32Z] [main] Version: 0.7.17-r1188
[2020-05-18T14:32Z] [main] CMD: /home/vagrant/local/bin/bwa mem -c 250 -M -t 1 -R @RG\tID:Test1\tPL:illumina\tPU:Test1\tSM:Test1 -v 1 /vagrant/tests/data/genomes/mm9/bwa/mm9.fa /tmp/bcbio/test_automated_output/fastq/atac_1.fq.gz /tmp/bcbio/test_automated_output/fastq/atac_2.fq.gz
[2020-05-18T14:32Z] [main] Real time: 0.084 sec; CPU: 0.076 sec
[2020-05-18T14:32Z] [V] 5036	07942999	MemUsage(size=476.711,rss=15.8008,peak=476.711)	AutoArrayMemUsage(memusage=337.486,peakmemusage=337.487,maxmem=1.75922e+13)	final
[2020-05-18T14:32Z] [V] flushing read ends lists...done.
[2020-05-18T14:32Z] [V] merging read ends lists/computing duplicates...done, time 01:14319799
[2020-05-18T14:32Z] [V] num dups 3
[2020-05-18T14:32Z] # bamsormadup
[2020-05-18T14:32Z] ##METRICS
[2020-05-18T14:32Z] LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATIONESTIMATED_LIBRARY_SIZE
[2020-05-18T14:32Z] Unknown Library	10	1199	2628	3	0	0	0.00124585	-1
[2020-05-18T14:32Z] ## HISTOGRAM
[2020-05-18T14:32Z] BIN	VALUE
[2020-05-18T14:32Z] [V] blocks generated in time 03:15919900
[2020-05-18T14:32Z] [V] number of blocks to be merged is 1 using 8192 blocks per input with block size 1048576
[2020-05-18T14:32Z] [V] 5036
[2020-05-18T14:32Z] [D]	md5	9d6e5b73f1862412765874eab15ccd41
[2020-05-18T14:32Z] [V] checksum ok
[2020-05-18T14:32Z] [V] blocks merged in time 01:06732699
[2020-05-18T14:32Z] [V] run time 04:22669300 (4.2267 s)	MemUsage(size=8351.52,rss=66.6797,peak=9375.53)
[2020-05-18T14:32Z] Index BAM file: Test1-sort.bam
[2020-05-18T14:32Z] Timing: disambiguation
[2020-05-18T14:32Z] multiprocessing: clean_chipseq_alignment
[2020-05-18T14:32Z] Shifting ATAC-seq alignments in /tmp/bcbio/test_automated_output/align/Test1/Test1-sort.bam to /tmp/bcbio/test_automated_output/bcbiotx/tmp71xjz1tx/Test1-sort-shifted.tmp.bam.
[2020-05-18T14:32Z] genome partition size for multiprocessing: 100000
[2020-05-18T14:32Z] Sort BAM file coordinate: Test1-sort-shifted.tmp.bam to Test1-sort-shifted.tmp.sorted.bam
[2020-05-18T14:32Z] Index BAM file: Test1-sort-shifted.bam
[2020-05-18T14:32Z] Remove contigs from /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted.bam
[2020-05-18T14:32Z] Index BAM file: Test1-sort-shifted_chrom.bam
[2020-05-18T14:32Z] Removing mitochondrial reads on chrM from /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom.bam.
[2020-05-18T14:32Z] Sort BAM file queryname: Test1-sort-shifted_chrom-noMito.bam to Test1-sort-shifted_chrom-noMito.nsorted.bam
[2020-05-18T14:32Z] Calculating ATAC-seq complexity metrics on /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.nsorted.bam, saving as /tmp/bcbio/test_automated_output/metrics/atac/Test1-atac-metrics.csv.
[2020-05-18T14:32Z] Removing multimapped reads from /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.bam.
[2020-05-18T14:32Z] sambamba 0.7.1
[2020-05-18T14:32Z]  by Artem Tarasov and Pjotr Prins (C) 2012-2019
[2020-05-18T14:32Z]     LDC 1.20.0 / DMD v2.090.1 / LLVM7.0.0 / bootstrap LDC - the LLVM D compiler (0.17.6)
[2020-05-18T14:32Z] Index BAM file: Test1-sort-shifted_chrom-noMito.unique.bam
[2020-05-18T14:32Z] Removing duplicates from /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique.bam, saving as /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam.
[2020-05-18T14:32Z] sambamba 0.7.1
[2020-05-18T14:32Z]  by Artem Tarasov and Pjotr Prins (C) 2012-2019
[2020-05-18T14:32Z]     LDC 1.20.0 / DMD v2.090.1 / LLVM7.0.0 / bootstrap LDC - the LLVM D compiler (0.17.6)
[2020-05-18T14:32Z] Index BAM file: Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam
[2020-05-18T14:32Z] Splitting NF regions from /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam.
[2020-05-18T14:32Z] sambamba 0.7.1
[2020-05-18T14:32Z]  by Artem Tarasov and Pjotr Prins (C) 2012-2019
[2020-05-18T14:32Z]     LDC 1.20.0 / DMD v2.090.1 / LLVM7.0.0 / bootstrap LDC - the LLVM D compiler (0.17.6)
[2020-05-18T14:32Z] Index BAM file: Test1-sort-shifted_chrom-noMito.unique-noduplicates-NF.bam
[2020-05-18T14:32Z] Splitting MN regions from /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam.
[2020-05-18T14:32Z] sambamba 0.7.1
[2020-05-18T14:32Z]  by Artem Tarasov and Pjotr Prins (C) 2012-2019
[2020-05-18T14:32Z]     LDC 1.20.0 / DMD v2.090.1 / LLVM7.0.0 / bootstrap LDC - the LLVM D compiler (0.17.6)
[2020-05-18T14:32Z] Index BAM file: Test1-sort-shifted_chrom-noMito.unique-noduplicates-MN.bam
[2020-05-18T14:32Z] Splitting DN regions from /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam.
[2020-05-18T14:32Z] sambamba 0.7.1
[2020-05-18T14:32Z]  by Artem Tarasov and Pjotr Prins (C) 2012-2019
[2020-05-18T14:32Z]     LDC 1.20.0 / DMD v2.090.1 / LLVM7.0.0 / bootstrap LDC - the LLVM D compiler (0.17.6)
[2020-05-18T14:32Z] Index BAM file: Test1-sort-shifted_chrom-noMito.unique-noduplicates-DN.bam
[2020-05-18T14:32Z] Splitting TN regions from /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam.
[2020-05-18T14:32Z] sambamba 0.7.1
[2020-05-18T14:32Z]  by Artem Tarasov and Pjotr Prins (C) 2012-2019
[2020-05-18T14:32Z]     LDC 1.20.0 / DMD v2.090.1 / LLVM7.0.0 / bootstrap LDC - the LLVM D compiler (0.17.6)
[2020-05-18T14:32Z] Index BAM file: Test1-sort-shifted_chrom-noMito.unique-noduplicates-TN.bam
[2020-05-18T14:32Z] Run bamCoverage in Test1
[2020-05-18T14:32Z] normalization: CPM
[2020-05-18T14:32Z] Traceback (most recent call last):
[2020-05-18T14:32Z]   File "/home/vagrant/local/bin/bamCoverage", line 12, in <module>
[2020-05-18T14:32Z]     main(args)
[2020-05-18T14:32Z]   File "/home/vagrant/local/share/bcbio/anaconda/lib/python3.6/site-packages/deeptools/bamCoverage.py", line 162, in main
[2020-05-18T14:32Z]     scale_factor = get_scale_factor(args, stats)
[2020-05-18T14:32Z]   File "/home/vagrant/local/share/bcbio/anaconda/lib/python3.6/site-packages/deeptools/getScaleFactor.py", line 279, in get_scale_factor
[2020-05-18T14:32Z]     scale_factor *= 1.0 / (million_reads_mapped)
[2020-05-18T14:32Z] ZeroDivisionError: float division by zero
[2020-05-18T14:32Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/vagrant/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/vagrant/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; /home/vagrant/local/bin/bamCoverage --bam /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam --outFileName /tmp/bcbio/test_automated_output/align/Test1/Test1.bw --binSize 20 --effectiveGenomeSize 16299 --smoothLength 60 --extendReads 150 --centerReads -p 1 --normalizeUsing CPM --ignoreForNormalization chrM
normalization: CPM
Traceback (most recent call last):
  File "/home/vagrant/local/bin/bamCoverage", line 12, in <module>
    main(args)
  File "/home/vagrant/local/share/bcbio/anaconda/lib/python3.6/site-packages/deeptools/bamCoverage.py", line 162, in main
    scale_factor = get_scale_factor(args, stats)
  File "/home/vagrant/local/share/bcbio/anaconda/lib/python3.6/site-packages/deeptools/getScaleFactor.py", line 279, in get_scale_factor
    scale_factor *= 1.0 / (million_reads_mapped)
ZeroDivisionError: float division by zero
' returned non-zero exit status 1.
[2020-05-18T14:32Z] /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam was too sparse to normalize,  falling back to non-normalized coverage.
[2020-05-18T14:32Z] Run bamCoverage in Test1
[2020-05-18T14:32Z] bamFilesList: ['/tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam']
[2020-05-18T14:32Z] binLength: 20
[2020-05-18T14:32Z] numberOfSamples: None
[2020-05-18T14:32Z] blackListFileName: None
[2020-05-18T14:32Z] skipZeroOverZero: False
[2020-05-18T14:32Z] bed_and_bin: False
[2020-05-18T14:32Z] genomeChunkSize: None
[2020-05-18T14:32Z] defaultFragmentLength: 150
[2020-05-18T14:32Z] numberOfProcessors: 1
[2020-05-18T14:32Z] verbose: False
[2020-05-18T14:32Z] region: None
[2020-05-18T14:32Z] bedFile: None
[2020-05-18T14:32Z] minMappingQuality: None
[2020-05-18T14:32Z] ignoreDuplicates: False
[2020-05-18T14:32Z] chrsToSkip: []
[2020-05-18T14:32Z] stepSize: 20
[2020-05-18T14:32Z] center_read: True
[2020-05-18T14:32Z] samFlag_include: None
[2020-05-18T14:32Z] samFlag_exclude: None
[2020-05-18T14:32Z] minFragmentLength: 0
[2020-05-18T14:32Z] maxFragmentLength: 0
[2020-05-18T14:32Z] zerosToNans: False
[2020-05-18T14:32Z] smoothLength: 60
[2020-05-18T14:32Z] save_data: False
[2020-05-18T14:32Z] out_file_for_raw_data: None
[2020-05-18T14:32Z] maxPairedFragmentLength: 600
[2020-05-18T14:32Z] Resource requests: macs2; memory: 8.00; cores: 1
[2020-05-18T14:32Z] Configuring 1 jobs to run, using 1 cores each with 8.00g of memory reserved for each job
[2020-05-18T14:32Z] Timing: peakcalling
[2020-05-18T14:32Z] multiprocessing: peakcalling
[2020-05-18T14:32Z] Counting alignments in /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates-NF.bam.
[2020-05-18T14:32Z] /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates-NF.bam has less than 1000, peak calling will fail so skip this fraction.
[2020-05-18T14:32Z] Counting alignments in /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates-MN.bam.
[2020-05-18T14:32Z] /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates-MN.bam has less than 1000, peak calling will fail so skip this fraction.
[2020-05-18T14:32Z] Counting alignments in /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates-DN.bam.
[2020-05-18T14:32Z] /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates-DN.bam has less than 1000, peak calling will fail so skip this fraction.
[2020-05-18T14:32Z] Counting alignments in /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates-TN.bam.
[2020-05-18T14:32Z] /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates-TN.bam has less than 1000, peak calling will fail so skip this fraction.
[2020-05-18T14:32Z] Counting alignments in /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam.
[2020-05-18T14:32Z] Running peak calling with macs2 on the full fraction of /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam.
[2020-05-18T14:32Z] ATAC-seq specified, using narrow peak settings.
[2020-05-18T14:32Z] macs2 for Test1-full
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50:
[2020-05-18T14:32Z] # Command line: callpeak -t /tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam --nomodel -f BAMPE -g 16299 -n Test1-full --bdg --nolambda --keep-dup all
[2020-05-18T14:32Z] # ARGUMENTS LIST:
[2020-05-18T14:32Z] # name = Test1-full
[2020-05-18T14:32Z] # format = BAMPE
[2020-05-18T14:32Z] # ChIP-seq file = ['/tmp/bcbio/test_automated_output/align/Test1/Test1-sort-shifted_chrom-noMito.unique-noduplicates.bam']
[2020-05-18T14:32Z] # control file = None
[2020-05-18T14:32Z] # effective genome size = 1.63e+04
[2020-05-18T14:32Z] # band width = 300
[2020-05-18T14:32Z] # model fold = [5, 50]
[2020-05-18T14:32Z] # qvalue cutoff = 5.00e-02
[2020-05-18T14:32Z] # The maximum gap between significant sites is assigned as the read length/tag size.
[2020-05-18T14:32Z] # The minimum length of peaks is assigned as the predicted fragment length "d".
[2020-05-18T14:32Z] # Larger dataset will be scaled towards smaller dataset.
[2020-05-18T14:32Z] # Range for calculating regional lambda is: 10000 bps
[2020-05-18T14:32Z] # Broad region calling is off
[2020-05-18T14:32Z] # Paired-End mode is on
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #1 read fragment files...
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #1 read treatment fragments...
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: 1199 fragments have been read.
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #1 mean fragment size is determined as 327.4 bp from treatment
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #1 fragment size = 327.4
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #1  total fragments in treatment: 1199
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #1 finished!
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #2 Build Peak Model...
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #2 Skipped...
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #3 Call peaks...
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: # local lambda is disabled!
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #3 !!!! DYNAMIC LAMBDA IS DISABLED !!!!
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #3 Pre-compute pvalue-qvalue table...
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #3 In the peak calling step, the following will be performed simultaneously:
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #3   Write bedGraph files for treatment pileup (after scaling if necessary)... Test1-full_treat_pileup.bdg
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #3   Write bedGraph files for control lambda (after scaling if necessary)... Test1-full_control_lambda.bdg
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #3   Pileup will be based on sequencing depth in treatment.
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #3 Call peaks for each chromosome...
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #4 Write output xls file... Test1-full_peaks.xls
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #4 Write peak in narrowPeak format file... Test1-full_peaks.narrowPeak
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: #4 Write summits bed file... Test1-full_summits.bed
[2020-05-18T14:32Z] INFO  @ Mon, 18 May 2020 10:32:50: Done!
[2020-05-18T14:32Z] Compressing and sorting /tmp/bcbio/test_automated_output/macs2/Test1-full/Test1-full_treat_pileup.bdg.
[2020-05-18T14:32Z] Compressing and sorting /tmp/bcbio/test_automated_output/macs2/Test1-full/Test1-full_control_lambda.bdg.
[2020-05-18T14:32Z] No suitable peak files found, skipping consensus peak calling.
[2020-05-18T14:32Z] multiprocessing: run_chipseq_count
[2020-05-18T14:32Z] Sort BAM file queryname: Test1-sort-shifted_chrom-noMito.unique-noduplicates-NF.bam to Test1-sort-shifted_chrom-noMito.unique-noduplicates-NF.nsorted.bam
Traceback (most recent call last):
  File "/home/vagrant/local/share/bcbio/anaconda/bin/bcbio_nextgen.py", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/vagrant/scripts/bcbio_nextgen.py", line 245, in <module>
    main(**kwargs)
  File "/vagrant/scripts/bcbio_nextgen.py", line 46, in main
    run_main(**kwargs)
  File "/vagrant/bcbio/pipeline/main.py", line 50, in run_main
    fc_dir, run_info_yaml)
  File "/vagrant/bcbio/pipeline/main.py", line 91, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File "/vagrant/bcbio/pipeline/main.py", line 388, in chipseqpipeline
    samples = run_parallel("run_chipseq_count", samples)
  File "/vagrant/bcbio/distributed/multi.py", line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File "/vagrant/bcbio/distributed/multi.py", line 86, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"], batch_size=1, backend="multiprocessing")(joblib.delayed(fn)(*x) for x in items):
  File "/home/vagrant/local/share/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 1029, in __call__
    if self.dispatch_one_batch(iterator):
  File "/home/vagrant/local/share/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 847, in dispatch_one_batch
    self._dispatch(tasks)
  File "/home/vagrant/local/share/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 765, in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
  File "/home/vagrant/local/share/bcbio/anaconda/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 206, in apply_async
    result = ImmediateResult(func)
  File "/home/vagrant/local/share/bcbio/anaconda/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 570, in __init__
    self.results = batch()
  File "/home/vagrant/local/share/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 253, in __call__
    for func, args, kwargs in self.items]
  File "/home/vagrant/local/share/bcbio/anaconda/lib/python3.6/site-packages/joblib/parallel.py", line 253, in <listcomp>
    for func, args, kwargs in self.items]
  File "/vagrant/bcbio/utils.py", line 55, in wrapper
    return f(*args, **kwargs)
  File "/vagrant/bcbio/distributed/multitasks.py", line 32, in run_chipseq_count
    return featureCounts.chipseq_count(*args)
  File "/vagrant/bcbio/rnaseq/featureCounts.py", line 75, in chipseq_count
    saf_file = os.path.splitext(consensus_file)[0] + ".saf"
  File "/home/vagrant/local/bin/../share/bcbio/anaconda/lib/python3.6/posixpath.py", line 122, in splitext
    p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not NoneType

Additional context
Discovered in the context of #3176
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@hackdna @naumenko-sa