Job ID = 6529114 SRX = SRX5709766 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: 00:08:02 33385313 reads; of these: 33385313 (100.00%) were unpaired; of these: 1177160 (3.53%) aligned 0 times 26912015 (80.61%) aligned exactly 1 time 5296138 (15.86%) aligned >1 times 96.47% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 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_sort_core] merging from 16 files... [bam_rmdupse_core] 7457612 / 32208153 = 0.2315 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, 30 Jun 2020 01:26:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.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, 30 Jun 2020 01:26:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:26:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:26:57: 1000000 INFO @ Tue, 30 Jun 2020 01:27:03: 2000000 INFO @ Tue, 30 Jun 2020 01:27:09: 3000000 INFO @ Tue, 30 Jun 2020 01:27:16: 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, 30 Jun 2020 01:27:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.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, 30 Jun 2020 01:27:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:27:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:22: 5000000 INFO @ Tue, 30 Jun 2020 01:27:28: 1000000 INFO @ Tue, 30 Jun 2020 01:27:28: 6000000 INFO @ Tue, 30 Jun 2020 01:27:34: 2000000 INFO @ Tue, 30 Jun 2020 01:27:35: 7000000 INFO @ Tue, 30 Jun 2020 01:27:41: 3000000 INFO @ Tue, 30 Jun 2020 01:27:42: 8000000 INFO @ Tue, 30 Jun 2020 01:27:47: 4000000 INFO @ Tue, 30 Jun 2020 01:27:48: 9000000 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, 30 Jun 2020 01:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.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, 30 Jun 2020 01:27:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:27:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:54: 5000000 INFO @ Tue, 30 Jun 2020 01:27:55: 10000000 INFO @ Tue, 30 Jun 2020 01:27:58: 1000000 INFO @ Tue, 30 Jun 2020 01:28:01: 6000000 INFO @ Tue, 30 Jun 2020 01:28:02: 11000000 INFO @ Tue, 30 Jun 2020 01:28:04: 2000000 INFO @ Tue, 30 Jun 2020 01:28:07: 7000000 INFO @ Tue, 30 Jun 2020 01:28:08: 12000000 INFO @ Tue, 30 Jun 2020 01:28:11: 3000000 INFO @ Tue, 30 Jun 2020 01:28:14: 8000000 INFO @ Tue, 30 Jun 2020 01:28:15: 13000000 INFO @ Tue, 30 Jun 2020 01:28:18: 4000000 INFO @ Tue, 30 Jun 2020 01:28:21: 9000000 INFO @ Tue, 30 Jun 2020 01:28:22: 14000000 INFO @ Tue, 30 Jun 2020 01:28:24: 5000000 INFO @ Tue, 30 Jun 2020 01:28:27: 10000000 INFO @ Tue, 30 Jun 2020 01:28:28: 15000000 INFO @ Tue, 30 Jun 2020 01:28:31: 6000000 INFO @ Tue, 30 Jun 2020 01:28:34: 11000000 INFO @ Tue, 30 Jun 2020 01:28:35: 16000000 INFO @ Tue, 30 Jun 2020 01:28:38: 7000000 INFO @ Tue, 30 Jun 2020 01:28:41: 12000000 INFO @ Tue, 30 Jun 2020 01:28:42: 17000000 INFO @ Tue, 30 Jun 2020 01:28:44: 8000000 INFO @ Tue, 30 Jun 2020 01:28:48: 18000000 INFO @ Tue, 30 Jun 2020 01:28:48: 13000000 INFO @ Tue, 30 Jun 2020 01:28:51: 9000000 INFO @ Tue, 30 Jun 2020 01:28:55: 19000000 INFO @ Tue, 30 Jun 2020 01:28:55: 14000000 INFO @ Tue, 30 Jun 2020 01:28:57: 10000000 INFO @ Tue, 30 Jun 2020 01:29:01: 20000000 INFO @ Tue, 30 Jun 2020 01:29:02: 15000000 INFO @ Tue, 30 Jun 2020 01:29:04: 11000000 INFO @ Tue, 30 Jun 2020 01:29:08: 21000000 INFO @ Tue, 30 Jun 2020 01:29:09: 16000000 INFO @ Tue, 30 Jun 2020 01:29:11: 12000000 INFO @ Tue, 30 Jun 2020 01:29:15: 22000000 INFO @ Tue, 30 Jun 2020 01:29:16: 17000000 INFO @ Tue, 30 Jun 2020 01:29:17: 13000000 INFO @ Tue, 30 Jun 2020 01:29:21: 23000000 INFO @ Tue, 30 Jun 2020 01:29:23: 18000000 INFO @ Tue, 30 Jun 2020 01:29:24: 14000000 INFO @ Tue, 30 Jun 2020 01:29:27: 24000000 INFO @ Tue, 30 Jun 2020 01:29:29: 19000000 INFO @ Tue, 30 Jun 2020 01:29:30: 15000000 INFO @ Tue, 30 Jun 2020 01:29:33: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:29:33: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:29:33: #1 total tags in treatment: 24750541 INFO @ Tue, 30 Jun 2020 01:29:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:29:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:29:33: #1 tags after filtering in treatment: 24750541 INFO @ Tue, 30 Jun 2020 01:29:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:29:33: #1 finished! INFO @ Tue, 30 Jun 2020 01:29:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:29:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:29:35: #2 number of paired peaks: 161 WARNING @ Tue, 30 Jun 2020 01:29:35: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 30 Jun 2020 01:29:35: start model_add_line... INFO @ Tue, 30 Jun 2020 01:29:35: start X-correlation... INFO @ Tue, 30 Jun 2020 01:29:35: end of X-cor INFO @ Tue, 30 Jun 2020 01:29:35: #2 finished! INFO @ Tue, 30 Jun 2020 01:29:35: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:29:35: #2 alternative fragment length(s) may be 1,19,585,595 bps INFO @ Tue, 30 Jun 2020 01:29:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.05_model.r WARNING @ Tue, 30 Jun 2020 01:29:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:29:35: #2 You may need to consider one of the other alternative d(s): 1,19,585,595 WARNING @ Tue, 30 Jun 2020 01:29:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:29:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:29:36: 20000000 INFO @ Tue, 30 Jun 2020 01:29:37: 16000000 INFO @ Tue, 30 Jun 2020 01:29:43: 21000000 INFO @ Tue, 30 Jun 2020 01:29:43: 17000000 INFO @ Tue, 30 Jun 2020 01:29:50: 22000000 INFO @ Tue, 30 Jun 2020 01:29:50: 18000000 INFO @ Tue, 30 Jun 2020 01:29:56: 19000000 INFO @ Tue, 30 Jun 2020 01:29:56: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:30:03: 20000000 INFO @ Tue, 30 Jun 2020 01:30:03: 24000000 INFO @ Tue, 30 Jun 2020 01:30:08: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:30:08: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:30:08: #1 total tags in treatment: 24750541 INFO @ Tue, 30 Jun 2020 01:30:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:30:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:30:09: #1 tags after filtering in treatment: 24750541 INFO @ Tue, 30 Jun 2020 01:30:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:30:09: #1 finished! INFO @ Tue, 30 Jun 2020 01:30:09: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:30:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:30:09: 21000000 INFO @ Tue, 30 Jun 2020 01:30:10: #2 number of paired peaks: 161 WARNING @ Tue, 30 Jun 2020 01:30:10: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 30 Jun 2020 01:30:10: start model_add_line... INFO @ Tue, 30 Jun 2020 01:30:11: start X-correlation... INFO @ Tue, 30 Jun 2020 01:30:11: end of X-cor INFO @ Tue, 30 Jun 2020 01:30:11: #2 finished! INFO @ Tue, 30 Jun 2020 01:30:11: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:30:11: #2 alternative fragment length(s) may be 1,19,585,595 bps INFO @ Tue, 30 Jun 2020 01:30:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.10_model.r WARNING @ Tue, 30 Jun 2020 01:30:11: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:30:11: #2 You may need to consider one of the other alternative d(s): 1,19,585,595 WARNING @ Tue, 30 Jun 2020 01:30:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:30:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:30:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:30:15: 22000000 INFO @ Tue, 30 Jun 2020 01:30:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:30:22: 23000000 INFO @ Tue, 30 Jun 2020 01:30:28: 24000000 INFO @ Tue, 30 Jun 2020 01:30:32: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:30:32: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:30:32: #1 total tags in treatment: 24750541 INFO @ Tue, 30 Jun 2020 01:30:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:30:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:30:33: #1 tags after filtering in treatment: 24750541 INFO @ Tue, 30 Jun 2020 01:30:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:30:33: #1 finished! INFO @ Tue, 30 Jun 2020 01:30:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:30:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:30:35: #2 number of paired peaks: 161 WARNING @ Tue, 30 Jun 2020 01:30:35: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 30 Jun 2020 01:30:35: start model_add_line... INFO @ Tue, 30 Jun 2020 01:30:35: start X-correlation... INFO @ Tue, 30 Jun 2020 01:30:35: end of X-cor INFO @ Tue, 30 Jun 2020 01:30:35: #2 finished! INFO @ Tue, 30 Jun 2020 01:30:35: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:30:35: #2 alternative fragment length(s) may be 1,19,585,595 bps INFO @ Tue, 30 Jun 2020 01:30:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.20_model.r WARNING @ Tue, 30 Jun 2020 01:30:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:30:35: #2 You may need to consider one of the other alternative d(s): 1,19,585,595 WARNING @ Tue, 30 Jun 2020 01:30:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:30:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:30:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:30:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:30:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:30:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.05_summits.bed INFO @ Tue, 30 Jun 2020 01:30:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:30:53: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:31:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:31:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:31:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.10_summits.bed INFO @ Tue, 30 Jun 2020 01:31:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:31:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:31:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:31:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:31:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709766/SRX5709766.20_summits.bed INFO @ Tue, 30 Jun 2020 01:31:35: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling