Job ID = 6626559 SRX = SRX7262243 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:02:16 10477384 reads; of these: 10477384 (100.00%) were unpaired; of these: 1582472 (15.10%) aligned 0 times 7406568 (70.69%) aligned exactly 1 time 1488344 (14.21%) aligned >1 times 84.90% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 794517 / 8894912 = 0.0893 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 07:36:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.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 07:36:04: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:36:04: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:36:10: 1000000 INFO @ Tue, 14 Jul 2020 07:36:17: 2000000 INFO @ Tue, 14 Jul 2020 07:36:23: 3000000 INFO @ Tue, 14 Jul 2020 07:36:29: 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 @ Tue, 14 Jul 2020 07:36:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.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 07:36:34: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:36:34: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:36:36: 5000000 INFO @ Tue, 14 Jul 2020 07:36:40: 1000000 INFO @ Tue, 14 Jul 2020 07:36:42: 6000000 INFO @ Tue, 14 Jul 2020 07:36:47: 2000000 INFO @ Tue, 14 Jul 2020 07:36:49: 7000000 INFO @ Tue, 14 Jul 2020 07:36:53: 3000000 INFO @ Tue, 14 Jul 2020 07:36:56: 8000000 INFO @ Tue, 14 Jul 2020 07:36:56: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:36:56: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:36:56: #1 total tags in treatment: 8100395 INFO @ Tue, 14 Jul 2020 07:36:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:36:56: #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 07:36:56: #1 tags after filtering in treatment: 8100395 INFO @ Tue, 14 Jul 2020 07:36:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:36:56: #1 finished! INFO @ Tue, 14 Jul 2020 07:36:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:36:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:36:57: #2 number of paired peaks: 336 WARNING @ Tue, 14 Jul 2020 07:36:57: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Tue, 14 Jul 2020 07:36:57: start model_add_line... INFO @ Tue, 14 Jul 2020 07:36:57: start X-correlation... INFO @ Tue, 14 Jul 2020 07:36:57: end of X-cor INFO @ Tue, 14 Jul 2020 07:36:57: #2 finished! INFO @ Tue, 14 Jul 2020 07:36:57: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:36:57: #2 alternative fragment length(s) may be 4,47,486,558,583 bps INFO @ Tue, 14 Jul 2020 07:36:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.05_model.r WARNING @ Tue, 14 Jul 2020 07:36:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:36:57: #2 You may need to consider one of the other alternative d(s): 4,47,486,558,583 WARNING @ Tue, 14 Jul 2020 07:36:57: #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 07:36:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:37:00: 4000000 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 07:37:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.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 07:37:04: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:37:04: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:37:06: 5000000 INFO @ Tue, 14 Jul 2020 07:37:10: 1000000 INFO @ Tue, 14 Jul 2020 07:37:13: 6000000 INFO @ Tue, 14 Jul 2020 07:37:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:37:17: 2000000 INFO @ Tue, 14 Jul 2020 07:37:20: 7000000 INFO @ Tue, 14 Jul 2020 07:37:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:37:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:37:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.05_summits.bed INFO @ Tue, 14 Jul 2020 07:37:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (558 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:37:24: 3000000 INFO @ Tue, 14 Jul 2020 07:37:26: 8000000 INFO @ Tue, 14 Jul 2020 07:37:27: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:37:27: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:37:27: #1 total tags in treatment: 8100395 INFO @ Tue, 14 Jul 2020 07:37:27: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:37:27: #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 07:37:27: #1 tags after filtering in treatment: 8100395 INFO @ Tue, 14 Jul 2020 07:37:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:37:27: #1 finished! INFO @ Tue, 14 Jul 2020 07:37:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:37:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:37:28: #2 number of paired peaks: 336 WARNING @ Tue, 14 Jul 2020 07:37:28: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Tue, 14 Jul 2020 07:37:28: start model_add_line... INFO @ Tue, 14 Jul 2020 07:37:28: start X-correlation... INFO @ Tue, 14 Jul 2020 07:37:28: end of X-cor INFO @ Tue, 14 Jul 2020 07:37:28: #2 finished! INFO @ Tue, 14 Jul 2020 07:37:28: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:37:28: #2 alternative fragment length(s) may be 4,47,486,558,583 bps INFO @ Tue, 14 Jul 2020 07:37:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.10_model.r WARNING @ Tue, 14 Jul 2020 07:37:28: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:37:28: #2 You may need to consider one of the other alternative d(s): 4,47,486,558,583 WARNING @ Tue, 14 Jul 2020 07:37:28: #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 07:37:28: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:37:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:37:30: 4000000 INFO @ Tue, 14 Jul 2020 07:37:36: 5000000 INFO @ Tue, 14 Jul 2020 07:37:43: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:37:44: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:37:49: 7000000 INFO @ Tue, 14 Jul 2020 07:37:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:37:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:37:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.10_summits.bed INFO @ Tue, 14 Jul 2020 07:37:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (339 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:37:55: 8000000 INFO @ Tue, 14 Jul 2020 07:37:56: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:37:56: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:37:56: #1 total tags in treatment: 8100395 INFO @ Tue, 14 Jul 2020 07:37:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:37:56: #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 07:37:56: #1 tags after filtering in treatment: 8100395 INFO @ Tue, 14 Jul 2020 07:37:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:37:56: #1 finished! INFO @ Tue, 14 Jul 2020 07:37:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:37:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:37:56: #2 number of paired peaks: 336 WARNING @ Tue, 14 Jul 2020 07:37:56: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Tue, 14 Jul 2020 07:37:56: start model_add_line... INFO @ Tue, 14 Jul 2020 07:37:56: start X-correlation... INFO @ Tue, 14 Jul 2020 07:37:56: end of X-cor INFO @ Tue, 14 Jul 2020 07:37:56: #2 finished! INFO @ Tue, 14 Jul 2020 07:37:56: #2 predicted fragment length is 47 bps INFO @ Tue, 14 Jul 2020 07:37:56: #2 alternative fragment length(s) may be 4,47,486,558,583 bps INFO @ Tue, 14 Jul 2020 07:37:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.20_model.r WARNING @ Tue, 14 Jul 2020 07:37:56: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:37:56: #2 You may need to consider one of the other alternative d(s): 4,47,486,558,583 WARNING @ Tue, 14 Jul 2020 07:37:56: #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 07:37:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:37:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:38:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:38:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:38:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:38:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7262243/SRX7262243.20_summits.bed INFO @ Tue, 14 Jul 2020 07:38:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 13 millis CompletedMACS2peakCalling