Closed pranathivemuri closed 4 years ago
pranathivemuri
commented
4 years ago pranathivemuri
commented
4 years ago I ran tests with test_bam.config and test_tenx_gz.config locally, both pass but for 1) the 2nd bam is not processed for 2) fastp and the next processes don't even run
(nextflow) ➜ kmermaid git:(pranathi-10x-gz) ✗ nextflow run main.nf -c conf/test_bam.config
N E X T F L O W ~ version 19.07.0
Launching `main.nf` [festering_rubens] - revision: ec64a7b804
[2m----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/kmermaid v1.0.0dev
----------------------------------------------------
Run Name : festering_rubens
BAM : [https://github.com/nf-core/test-datasets/raw/kmermaid/testdata/10x-example/possorted_genome_bam.bam, https://github.com/nf-core/test-datasets/raw/olgabot/kmermaid-unaligned-tgz-v2/testdata/mouse_brown_fat_ptprc_plus_unaligned/outs/possorted_genome_bam.bam]
Skip trimming? : false
K-mer sizes : 3,9
Molecule : dna,protein,dayhoff
Log2 Sketch Sizes : 2,4
One Sig per Record: true
Track Abundance : false
Max Resources : 6 GB memory, 2 cpus, 2d time per job
Output dir : ./results
Launch dir : /Users/pranathivemuri/czbiohub/kmermaid
Working dir : /Users/pranathivemuri/czbiohub/kmermaid/work
Script dir : /Users/pranathivemuri/czbiohub/kmermaid
User : pranathivemuri
Config Profile : standard
Config Description: Minimal test dataset to check pipeline function
[0m----------------------------------------------------
executor > local (11)
[ea/344c44] process > get_software_versions [100%] 1 of 1 ✔
[55/d18a8d] process > bam2fasta (1) [100%] 1 of 1 ✔
[e2/37b93b] process > fastp (possorted_genome_bam) [100%] 1 of 1 ✔
[04/b774ac] process > sourmash_compute_sketch_fastx_nucleotide (possorted_genome_bam_molecule-dna_ksize-9_log2sketchsize-2_trackabundance-false) [100%] 4 of 4 ✔
[dc/458fb0] process > sourmash_compare_sketches (molecule-dna_ksize-3_log2sketchsize-2_trackabundance-false) [100%] 4 of 4 ✔
[0;35mWarning, pipeline completed, but with errored process(es)
[0;31mNumber of ignored errored process(es) : 0
[0;32mNumber of successfully ran process(es) : 11
[0;35m[nf-core/kmermaid] Pipeline completed successfully
WARN: Task runtime metrics are not reported when using macOS without a container engine
(nextflow) ➜ kmermaid git:(pranathi-10x-gz) ✗ nextflow run main.nf -c conf/test_tenx_tgz.config
N E X T F L O W ~ version 19.07.0
Launching `main.nf` [backstabbing_hilbert] - revision: ec64a7b804
[2m----------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/kmermaid v1.0.0dev
----------------------------------------------------
Run Name : backstabbing_hilbert
Skip trimming? : false
K-mer sizes : 3,9
Molecule : dna,protein,dayhoff
Log2 Sketch Sizes : 2,4
One Sig per Record: true
Track Abundance : false
10x .tgz : [https://github.com/nf-core/test-datasets/raw/kmermaid/testdata/mouse_lung.tgz, https://github.com/nf-core/test-datasets/raw/olgabot/kmermaid-unaligned-tgz-v3/testdata/mouse_brown_fat_ptprc_plus_unaligned.tgz]
10x SAM tags : CB,UB,XC,XM,RG
10x Cell pattern : (CB|CB):Z:([ACGT]+)(\-1)?
10x UMI pattern : (UB|XB):Z:([ACGT]+)
Min UMI/cell : 10
Max Resources : 6 GB memory, 2 cpus, 2d time per job
Output dir : ./results
Launch dir : /Users/pranathivemuri/czbiohub/kmermaid
Working dir : /Users/pranathivemuri/czbiohub/kmermaid/work
Script dir : /Users/pranathivemuri/czbiohub/kmermaid
User : pranathivemuri
Config Profile : standard
Config Description: Minimal test dataset to check pipeline function
[0m----------------------------------------------------
executor > local (12)
[c8/7e80f3] process > get_software_versions [100%] 1 of 1 ✔
[59/64d418] process > tenx_tgz_extract_bam (mouse_brown_fat_ptprc_plus_unaligned) [100%] 2 of 2 ✔
[ed/2b5043] process > samtools_fastq_aligned (mouse_brown_fat_ptprc_plus_unaligned) [100%] 2 of 2 ✔
[a7/2039d6] process > samtools_fastq_unaligned (mouse_brown_fat_ptprc_plus_unaligned) [100%] 2 of 2 ✔
[89/82046a] process > count_umis_per_cell (mouse_brown_fat_ptprc_plus_unaligned__aligned) [100%] 2 of 2 ✔
[d1/dbc2d3] process > extract_per_cell_fastqs (mouse_brown_fat_ptprc_plus_unaligned__aligned) [100%] 3 of 3 ✔
[- ] process > fastp -
[- ] process > sourmash_compute_sketch_fastx_nucleotide -
[- ] process > sourmash_compare_sketches -
[0;35mWarning, pipeline completed, but with errored process(es)
[0;31mNumber of ignored errored process(es) : 0
[0;32mNumber of successfully ran process(es) : 12
[0;35m[nf-core/kmermaid] Pipeline completed successfully
WARN: Task runtime metrics are not reported when using macOS without a container engine
For bam.config, I think the error could be because the filenames are same possorted_genome_bam.bam
For the fastp, and next processes not getting executed for test_tenx_gz.config, I think its because of these lines here. // Make per-cell fastqs into a flat channel that matches the read channels of yore per_channel_cell_reads_ch .dump(tag: 'per_channel_cell_reads_ch') .flatten() .filter{ it -> it.size() > 0 } // each item is just a single file, no need to do it[1] .map{ it -> tuple(it.simpleName, file(it)) } .dump(tag: 'per_cell_fastqs_ch') .set{ per_cell_fastqs_ch }
olgabot
commented
4 years ago
- For bam.config, I think the error could be because the filenames are same possorted_genome_bam.bam
Can there be a test added with different filenames?
- For the fastp, and next processes not getting executed for test_tenx_gz.config, I think its because of these lines here. // Make per-cell fastqs into a flat channel that matches the read channels of yore per_channel_cell_reads_ch .dump(tag: 'per_channel_cell_reads_ch') .flatten() .filter{ it -> it.size() > 0 } // each item is just a single file, no need to do it[1] .map{ it -> tuple(it.simpleName, file(it)) } .dump(tag: 'per_cell_fastqs_ch') .set{ per_cell_fastqs_ch }
Does that mean that all of the fastqs are empty?
snafees
commented
4 years ago Hey @pranathivemuri, just ran from your branch and this is the error I get:
pranathivemuri
commented
4 years ago @snafees looks like bam2fasta is not up to date on this docker container. could you pull the docker container and retry on lrrr
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