Job ID = 6626383 SRX = SRX7262220 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 864720 spots for SRR10581843/SRR10581843.sra Written 864720 spots for SRR10581843/SRR10581843.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626401 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:20 864720 reads; of these: 864720 (100.00%) were unpaired; of these: 217813 (25.19%) aligned 0 times 412828 (47.74%) aligned exactly 1 time 234079 (27.07%) aligned >1 times 74.81% overall alignment rate Time searching: 00:00:20 Overall time: 00:00:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 213112 / 646907 = 0.3294 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 06:57:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 06:57:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:57:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:57:59: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:57:59: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:57:59: #1 total tags in treatment: 433795 INFO @ Tue, 14 Jul 2020 06:57:59: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:57:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 06:57:59: #1 tags after filtering in treatment: 433795 INFO @ Tue, 14 Jul 2020 06:57:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:57:59: #1 finished! INFO @ Tue, 14 Jul 2020 06:57:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:57:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:57:59: #2 number of paired peaks: 524 WARNING @ Tue, 14 Jul 2020 06:57:59: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Tue, 14 Jul 2020 06:57:59: start model_add_line... INFO @ Tue, 14 Jul 2020 06:57:59: start X-correlation... INFO @ Tue, 14 Jul 2020 06:57:59: end of X-cor INFO @ Tue, 14 Jul 2020 06:57:59: #2 finished! INFO @ Tue, 14 Jul 2020 06:57:59: #2 predicted fragment length is 45 bps INFO @ Tue, 14 Jul 2020 06:57:59: #2 alternative fragment length(s) may be 45,116,252,356,451,501,531,593 bps INFO @ Tue, 14 Jul 2020 06:57:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.05_model.r WARNING @ Tue, 14 Jul 2020 06:57:59: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:57:59: #2 You may need to consider one of the other alternative d(s): 45,116,252,356,451,501,531,593 WARNING @ Tue, 14 Jul 2020 06:57:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 06:57:59: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:57:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 06:58:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:58:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.05_peaks.xls INFO @ Tue, 14 Jul 2020 06:58:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:58:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.05_summits.bed INFO @ Tue, 14 Jul 2020 06:58:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 13 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 06:58:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 06:58:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:58:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:58:28: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:58:28: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:58:28: #1 total tags in treatment: 433795 INFO @ Tue, 14 Jul 2020 06:58:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:58:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 06:58:28: #1 tags after filtering in treatment: 433795 INFO @ Tue, 14 Jul 2020 06:58:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:58:28: #1 finished! INFO @ Tue, 14 Jul 2020 06:58:28: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:58:28: #2 number of paired peaks: 524 WARNING @ Tue, 14 Jul 2020 06:58:28: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Tue, 14 Jul 2020 06:58:28: start model_add_line... INFO @ Tue, 14 Jul 2020 06:58:28: start X-correlation... INFO @ Tue, 14 Jul 2020 06:58:28: end of X-cor INFO @ Tue, 14 Jul 2020 06:58:28: #2 finished! INFO @ Tue, 14 Jul 2020 06:58:28: #2 predicted fragment length is 45 bps INFO @ Tue, 14 Jul 2020 06:58:28: #2 alternative fragment length(s) may be 45,116,252,356,451,501,531,593 bps INFO @ Tue, 14 Jul 2020 06:58:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.10_model.r WARNING @ Tue, 14 Jul 2020 06:58:28: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:58:28: #2 You may need to consider one of the other alternative d(s): 45,116,252,356,451,501,531,593 WARNING @ Tue, 14 Jul 2020 06:58:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 06:58:28: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 06:58:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:58:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.10_peaks.xls INFO @ Tue, 14 Jul 2020 06:58:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:58:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.10_summits.bed INFO @ Tue, 14 Jul 2020 06:58:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (100 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 06:58:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 14 Jul 2020 06:58:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:58:55: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 06:58:58: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:58:58: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:58:58: #1 total tags in treatment: 433795 INFO @ Tue, 14 Jul 2020 06:58:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:58:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 06:58:58: #1 tags after filtering in treatment: 433795 INFO @ Tue, 14 Jul 2020 06:58:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:58:58: #1 finished! INFO @ Tue, 14 Jul 2020 06:58:58: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:58:58: #2 number of paired peaks: 524 WARNING @ Tue, 14 Jul 2020 06:58:58: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Tue, 14 Jul 2020 06:58:58: start model_add_line... INFO @ Tue, 14 Jul 2020 06:58:58: start X-correlation... INFO @ Tue, 14 Jul 2020 06:58:58: end of X-cor INFO @ Tue, 14 Jul 2020 06:58:58: #2 finished! INFO @ Tue, 14 Jul 2020 06:58:58: #2 predicted fragment length is 45 bps INFO @ Tue, 14 Jul 2020 06:58:58: #2 alternative fragment length(s) may be 45,116,252,356,451,501,531,593 bps INFO @ Tue, 14 Jul 2020 06:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.20_model.r WARNING @ Tue, 14 Jul 2020 06:58:58: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:58:58: #2 You may need to consider one of the other alternative d(s): 45,116,252,356,451,501,531,593 WARNING @ Tue, 14 Jul 2020 06:58:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 06:58:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:58:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 06:58:59: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:59:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.20_peaks.xls INFO @ Tue, 14 Jul 2020 06:59:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:59:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262220/SRX7262220.20_summits.bed INFO @ Tue, 14 Jul 2020 06:59:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (62 records, 4 fields): 12 millis CompletedMACS2peakCalling