Job ID = 14158066 SRX = SRX10569196 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: 00:10:38 27302513 reads; of these: 27302513 (100.00%) were unpaired; of these: 9580605 (35.09%) aligned 0 times 14250781 (52.20%) aligned exactly 1 time 3471127 (12.71%) aligned >1 times 64.91% overall alignment rate Time searching: 00:10:38 Overall time: 00:10:38 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 8 files... [bam_rmdupse_core] 2424590 / 17721908 = 0.1368 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.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 @ Wed, 08 Dec 2021 14:27:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:27:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:28:02: 1000000 INFO @ Wed, 08 Dec 2021 14:28:12: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:28:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.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 @ Wed, 08 Dec 2021 14:28:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:28:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:28:22: 3000000 INFO @ Wed, 08 Dec 2021 14:28:33: 4000000 INFO @ Wed, 08 Dec 2021 14:28:36: 1000000 INFO @ Wed, 08 Dec 2021 14:28:43: 5000000 INFO @ Wed, 08 Dec 2021 14:28:49: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:28:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.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 @ Wed, 08 Dec 2021 14:28:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:28:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:28:53: 6000000 INFO @ Wed, 08 Dec 2021 14:29:02: 3000000 INFO @ Wed, 08 Dec 2021 14:29:04: 7000000 INFO @ Wed, 08 Dec 2021 14:29:06: 1000000 INFO @ Wed, 08 Dec 2021 14:29:14: 8000000 INFO @ Wed, 08 Dec 2021 14:29:15: 4000000 INFO @ Wed, 08 Dec 2021 14:29:20: 2000000 INFO @ Wed, 08 Dec 2021 14:29:25: 9000000 INFO @ Wed, 08 Dec 2021 14:29:28: 5000000 INFO @ Wed, 08 Dec 2021 14:29:34: 3000000 INFO @ Wed, 08 Dec 2021 14:29:35: 10000000 INFO @ Wed, 08 Dec 2021 14:29:41: 6000000 INFO @ Wed, 08 Dec 2021 14:29:45: 11000000 INFO @ Wed, 08 Dec 2021 14:29:47: 4000000 INFO @ Wed, 08 Dec 2021 14:29:54: 7000000 INFO @ Wed, 08 Dec 2021 14:29:56: 12000000 INFO @ Wed, 08 Dec 2021 14:30:00: 5000000 INFO @ Wed, 08 Dec 2021 14:30:06: 13000000 INFO @ Wed, 08 Dec 2021 14:30:06: 8000000 INFO @ Wed, 08 Dec 2021 14:30:13: 6000000 INFO @ Wed, 08 Dec 2021 14:30:15: 14000000 INFO @ Wed, 08 Dec 2021 14:30:19: 9000000 INFO @ Wed, 08 Dec 2021 14:30:25: 15000000 INFO @ Wed, 08 Dec 2021 14:30:27: 7000000 INFO @ Wed, 08 Dec 2021 14:30:28: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 14:30:28: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 14:30:28: #1 total tags in treatment: 15297318 INFO @ Wed, 08 Dec 2021 14:30:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:30:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:30:28: #1 tags after filtering in treatment: 15297318 INFO @ Wed, 08 Dec 2021 14:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:30:28: #1 finished! INFO @ Wed, 08 Dec 2021 14:30:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:30:29: #2 number of paired peaks: 290 WARNING @ Wed, 08 Dec 2021 14:30:29: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Wed, 08 Dec 2021 14:30:29: start model_add_line... INFO @ Wed, 08 Dec 2021 14:30:29: start X-correlation... INFO @ Wed, 08 Dec 2021 14:30:29: end of X-cor INFO @ Wed, 08 Dec 2021 14:30:29: #2 finished! INFO @ Wed, 08 Dec 2021 14:30:29: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 14:30:29: #2 alternative fragment length(s) may be 2,48,571 bps INFO @ Wed, 08 Dec 2021 14:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.05_model.r WARNING @ Wed, 08 Dec 2021 14:30:29: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:30:29: #2 You may need to consider one of the other alternative d(s): 2,48,571 WARNING @ Wed, 08 Dec 2021 14:30:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:30:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:30:32: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:30:39: 8000000 INFO @ Wed, 08 Dec 2021 14:30:45: 11000000 INFO @ Wed, 08 Dec 2021 14:30:51: 9000000 INFO @ Wed, 08 Dec 2021 14:30:57: 12000000 INFO @ Wed, 08 Dec 2021 14:31:04: 10000000 INFO @ Wed, 08 Dec 2021 14:31:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:31:10: 13000000 INFO @ Wed, 08 Dec 2021 14:31:16: 11000000 INFO @ Wed, 08 Dec 2021 14:31:23: 14000000 INFO @ Wed, 08 Dec 2021 14:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.05_summits.bed INFO @ Wed, 08 Dec 2021 14:31:24: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (663 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:31:29: 12000000 INFO @ Wed, 08 Dec 2021 14:31:37: 15000000 INFO @ Wed, 08 Dec 2021 14:31:40: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 14:31:40: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 14:31:40: #1 total tags in treatment: 15297318 INFO @ Wed, 08 Dec 2021 14:31:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:31:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:31:41: #1 tags after filtering in treatment: 15297318 INFO @ Wed, 08 Dec 2021 14:31:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:31:41: #1 finished! INFO @ Wed, 08 Dec 2021 14:31:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:31:41: 13000000 INFO @ Wed, 08 Dec 2021 14:31:42: #2 number of paired peaks: 290 WARNING @ Wed, 08 Dec 2021 14:31:42: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Wed, 08 Dec 2021 14:31:42: start model_add_line... INFO @ Wed, 08 Dec 2021 14:31:42: start X-correlation... INFO @ Wed, 08 Dec 2021 14:31:42: end of X-cor INFO @ Wed, 08 Dec 2021 14:31:42: #2 finished! INFO @ Wed, 08 Dec 2021 14:31:42: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 14:31:42: #2 alternative fragment length(s) may be 2,48,571 bps INFO @ Wed, 08 Dec 2021 14:31:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.10_model.r WARNING @ Wed, 08 Dec 2021 14:31:42: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:31:42: #2 You may need to consider one of the other alternative d(s): 2,48,571 WARNING @ Wed, 08 Dec 2021 14:31:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:31:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:31:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:31:54: 14000000 INFO @ Wed, 08 Dec 2021 14:32:07: 15000000 INFO @ Wed, 08 Dec 2021 14:32:10: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 14:32:10: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 14:32:10: #1 total tags in treatment: 15297318 INFO @ Wed, 08 Dec 2021 14:32:10: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:32:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:32:10: #1 tags after filtering in treatment: 15297318 INFO @ Wed, 08 Dec 2021 14:32:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:32:10: #1 finished! INFO @ Wed, 08 Dec 2021 14:32:10: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:32:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:32:12: #2 number of paired peaks: 290 WARNING @ Wed, 08 Dec 2021 14:32:12: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Wed, 08 Dec 2021 14:32:12: start model_add_line... INFO @ Wed, 08 Dec 2021 14:32:12: start X-correlation... INFO @ Wed, 08 Dec 2021 14:32:12: end of X-cor INFO @ Wed, 08 Dec 2021 14:32:12: #2 finished! INFO @ Wed, 08 Dec 2021 14:32:12: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 14:32:12: #2 alternative fragment length(s) may be 2,48,571 bps INFO @ Wed, 08 Dec 2021 14:32:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.20_model.r WARNING @ Wed, 08 Dec 2021 14:32:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:32:12: #2 You may need to consider one of the other alternative d(s): 2,48,571 WARNING @ Wed, 08 Dec 2021 14:32:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:32:12: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:32:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:32:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:32:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:32:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:32:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.10_summits.bed INFO @ Wed, 08 Dec 2021 14:32:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (425 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:32:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:33:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:33:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:33:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569196/SRX10569196.20_summits.bed INFO @ Wed, 08 Dec 2021 14:33:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 2 millis CompletedMACS2peakCalling