Job ID = 6497406 SRX = SRX466549 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:29:13 prefetch.2.10.7: 1) Downloading 'SRR1163615'... 2020-06-25T22:29:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:30:36 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:30:36 prefetch.2.10.7: 'SRR1163615' is valid 2020-06-25T22:30:36 prefetch.2.10.7: 1) 'SRR1163615' was downloaded successfully Read 7637125 spots for SRR1163615/SRR1163615.sra Written 7637125 spots for SRR1163615/SRR1163615.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:23 7637125 reads; of these: 7637125 (100.00%) were unpaired; of these: 301266 (3.94%) aligned 0 times 6419127 (84.05%) aligned exactly 1 time 916732 (12.00%) aligned >1 times 96.06% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 2467287 / 7335859 = 0.3363 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 @ Fri, 26 Jun 2020 07:34:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.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 @ Fri, 26 Jun 2020 07:34:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:34:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:34:24: 1000000 INFO @ Fri, 26 Jun 2020 07:34:30: 2000000 INFO @ Fri, 26 Jun 2020 07:34:36: 3000000 INFO @ Fri, 26 Jun 2020 07:34:42: 4000000 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 @ Fri, 26 Jun 2020 07:34:46: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:34:46: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:34:46: #1 total tags in treatment: 4868572 INFO @ Fri, 26 Jun 2020 07:34:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:34:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:34:46: #1 tags after filtering in treatment: 4868572 INFO @ Fri, 26 Jun 2020 07:34:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:34:46: #1 finished! INFO @ Fri, 26 Jun 2020 07:34:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:34:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:34:47: #2 number of paired peaks: 184 WARNING @ Fri, 26 Jun 2020 07:34:47: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 26 Jun 2020 07:34:47: start model_add_line... INFO @ Fri, 26 Jun 2020 07:34:47: start X-correlation... INFO @ Fri, 26 Jun 2020 07:34:47: end of X-cor INFO @ Fri, 26 Jun 2020 07:34:47: #2 finished! INFO @ Fri, 26 Jun 2020 07:34:47: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 07:34:47: #2 alternative fragment length(s) may be 4,42,465 bps INFO @ Fri, 26 Jun 2020 07:34:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.05_model.r WARNING @ Fri, 26 Jun 2020 07:34:47: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:34:47: #2 You may need to consider one of the other alternative d(s): 4,42,465 WARNING @ Fri, 26 Jun 2020 07:34:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:34:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:34:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:34:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.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 @ Fri, 26 Jun 2020 07:34:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:34:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:34:53: 1000000 INFO @ Fri, 26 Jun 2020 07:34:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:34:59: 2000000 INFO @ Fri, 26 Jun 2020 07:35:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:35:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:35:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.05_summits.bed INFO @ Fri, 26 Jun 2020 07:35:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:35:05: 3000000 INFO @ Fri, 26 Jun 2020 07:35:10: 4000000 INFO @ Fri, 26 Jun 2020 07:35:15: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:35:15: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:35:15: #1 total tags in treatment: 4868572 INFO @ Fri, 26 Jun 2020 07:35:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:35:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:35:15: #1 tags after filtering in treatment: 4868572 INFO @ Fri, 26 Jun 2020 07:35:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:35:15: #1 finished! INFO @ Fri, 26 Jun 2020 07:35:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:35:15: #2 number of paired peaks: 184 WARNING @ Fri, 26 Jun 2020 07:35:15: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 26 Jun 2020 07:35:15: start model_add_line... INFO @ Fri, 26 Jun 2020 07:35:15: start X-correlation... INFO @ Fri, 26 Jun 2020 07:35:15: end of X-cor INFO @ Fri, 26 Jun 2020 07:35:15: #2 finished! INFO @ Fri, 26 Jun 2020 07:35:15: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 07:35:15: #2 alternative fragment length(s) may be 4,42,465 bps INFO @ Fri, 26 Jun 2020 07:35:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.10_model.r WARNING @ Fri, 26 Jun 2020 07:35:15: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:35:15: #2 You may need to consider one of the other alternative d(s): 4,42,465 WARNING @ Fri, 26 Jun 2020 07:35:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:35:15: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:35:15: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 07:35:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.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 @ Fri, 26 Jun 2020 07:35:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:35:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:35:24: 1000000 INFO @ Fri, 26 Jun 2020 07:35:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:35:30: 2000000 INFO @ Fri, 26 Jun 2020 07:35:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:35:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:35:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.10_summits.bed INFO @ Fri, 26 Jun 2020 07:35:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (118 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:35:37: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:35:43: 4000000 INFO @ Fri, 26 Jun 2020 07:35:48: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:35:48: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:35:48: #1 total tags in treatment: 4868572 INFO @ Fri, 26 Jun 2020 07:35:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:35:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:35:48: #1 tags after filtering in treatment: 4868572 INFO @ Fri, 26 Jun 2020 07:35:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:35:48: #1 finished! INFO @ Fri, 26 Jun 2020 07:35:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:35:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:35:49: #2 number of paired peaks: 184 WARNING @ Fri, 26 Jun 2020 07:35:49: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 26 Jun 2020 07:35:49: start model_add_line... INFO @ Fri, 26 Jun 2020 07:35:49: start X-correlation... INFO @ Fri, 26 Jun 2020 07:35:49: end of X-cor INFO @ Fri, 26 Jun 2020 07:35:49: #2 finished! INFO @ Fri, 26 Jun 2020 07:35:49: #2 predicted fragment length is 42 bps INFO @ Fri, 26 Jun 2020 07:35:49: #2 alternative fragment length(s) may be 4,42,465 bps INFO @ Fri, 26 Jun 2020 07:35:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.20_model.r WARNING @ Fri, 26 Jun 2020 07:35:49: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:35:49: #2 You may need to consider one of the other alternative d(s): 4,42,465 WARNING @ Fri, 26 Jun 2020 07:35:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:35:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:35:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:35:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:36:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:36:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:36:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466549/SRX466549.20_summits.bed INFO @ Fri, 26 Jun 2020 07:36:05: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (40 records, 4 fields): 1 millis CompletedMACS2peakCalling