Job ID = 16434870 SRX = SRX10435507 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: 00:05:09 15101882 reads; of these: 15101882 (100.00%) were unpaired; of these: 4786704 (31.70%) aligned 0 times 8518294 (56.41%) aligned exactly 1 time 1796884 (11.90%) aligned >1 times 68.30% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 1975812 / 10315178 = 0.1915 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:15:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.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, 02 Aug 2022 10:15:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:15:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:15:08: 1000000 INFO @ Tue, 02 Aug 2022 10:15:14: 2000000 INFO @ Tue, 02 Aug 2022 10:15:19: 3000000 INFO @ Tue, 02 Aug 2022 10:15:25: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:15:31: 5000000 INFO @ Tue, 02 Aug 2022 10:15:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.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, 02 Aug 2022 10:15:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:15:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:15:37: 6000000 INFO @ Tue, 02 Aug 2022 10:15:39: 1000000 INFO @ Tue, 02 Aug 2022 10:15:44: 7000000 INFO @ Tue, 02 Aug 2022 10:15:46: 2000000 INFO @ Tue, 02 Aug 2022 10:15:50: 8000000 INFO @ Tue, 02 Aug 2022 10:15:52: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:15:52: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:15:52: #1 total tags in treatment: 8339366 INFO @ Tue, 02 Aug 2022 10:15:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:15:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:15:52: #1 tags after filtering in treatment: 8339366 INFO @ Tue, 02 Aug 2022 10:15:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:15:52: #1 finished! INFO @ Tue, 02 Aug 2022 10:15:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:15:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:15:53: #2 number of paired peaks: 369 WARNING @ Tue, 02 Aug 2022 10:15:53: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Tue, 02 Aug 2022 10:15:53: start model_add_line... INFO @ Tue, 02 Aug 2022 10:15:53: 3000000 INFO @ Tue, 02 Aug 2022 10:15:53: start X-correlation... INFO @ Tue, 02 Aug 2022 10:15:53: end of X-cor INFO @ Tue, 02 Aug 2022 10:15:53: #2 finished! INFO @ Tue, 02 Aug 2022 10:15:53: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:15:53: #2 alternative fragment length(s) may be 4,71,559 bps INFO @ Tue, 02 Aug 2022 10:15:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.05_model.r WARNING @ Tue, 02 Aug 2022 10:15:53: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:15:53: #2 You may need to consider one of the other alternative d(s): 4,71,559 WARNING @ Tue, 02 Aug 2022 10:15:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:15:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:15:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:16:00: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:16:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.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, 02 Aug 2022 10:16:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:16:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:16:07: 5000000 INFO @ Tue, 02 Aug 2022 10:16:09: 1000000 INFO @ Tue, 02 Aug 2022 10:16:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:16:14: 6000000 INFO @ Tue, 02 Aug 2022 10:16:16: 2000000 INFO @ Tue, 02 Aug 2022 10:16:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:16:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:16:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.05_summits.bed INFO @ Tue, 02 Aug 2022 10:16:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (542 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:16:20: 7000000 INFO @ Tue, 02 Aug 2022 10:16:22: 3000000 INFO @ Tue, 02 Aug 2022 10:16:27: 8000000 INFO @ Tue, 02 Aug 2022 10:16:30: 4000000 INFO @ Tue, 02 Aug 2022 10:16:30: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:16:30: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:16:30: #1 total tags in treatment: 8339366 INFO @ Tue, 02 Aug 2022 10:16:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:16:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:16:30: #1 tags after filtering in treatment: 8339366 INFO @ Tue, 02 Aug 2022 10:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:16:30: #1 finished! INFO @ Tue, 02 Aug 2022 10:16:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:16:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:16:30: #2 number of paired peaks: 369 WARNING @ Tue, 02 Aug 2022 10:16:30: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Tue, 02 Aug 2022 10:16:30: start model_add_line... INFO @ Tue, 02 Aug 2022 10:16:30: start X-correlation... INFO @ Tue, 02 Aug 2022 10:16:30: end of X-cor INFO @ Tue, 02 Aug 2022 10:16:30: #2 finished! INFO @ Tue, 02 Aug 2022 10:16:30: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:16:30: #2 alternative fragment length(s) may be 4,71,559 bps INFO @ Tue, 02 Aug 2022 10:16:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.10_model.r WARNING @ Tue, 02 Aug 2022 10:16:30: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:16:30: #2 You may need to consider one of the other alternative d(s): 4,71,559 WARNING @ Tue, 02 Aug 2022 10:16:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:16:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:16:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:16:36: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:16:43: 6000000 INFO @ Tue, 02 Aug 2022 10:16:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:16:49: 7000000 INFO @ Tue, 02 Aug 2022 10:16:55: 8000000 INFO @ Tue, 02 Aug 2022 10:16:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:16:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:16:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.10_summits.bed INFO @ Tue, 02 Aug 2022 10:16:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (393 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:16:57: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:16:57: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:16:57: #1 total tags in treatment: 8339366 INFO @ Tue, 02 Aug 2022 10:16:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:16:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:16:57: #1 tags after filtering in treatment: 8339366 INFO @ Tue, 02 Aug 2022 10:16:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:16:57: #1 finished! INFO @ Tue, 02 Aug 2022 10:16:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:16:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:16:58: #2 number of paired peaks: 369 WARNING @ Tue, 02 Aug 2022 10:16:58: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Tue, 02 Aug 2022 10:16:58: start model_add_line... INFO @ Tue, 02 Aug 2022 10:16:58: start X-correlation... INFO @ Tue, 02 Aug 2022 10:16:58: end of X-cor INFO @ Tue, 02 Aug 2022 10:16:58: #2 finished! INFO @ Tue, 02 Aug 2022 10:16:58: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:16:58: #2 alternative fragment length(s) may be 4,71,559 bps INFO @ Tue, 02 Aug 2022 10:16:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.20_model.r WARNING @ Tue, 02 Aug 2022 10:16:58: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:16:58: #2 You may need to consider one of the other alternative d(s): 4,71,559 WARNING @ Tue, 02 Aug 2022 10:16:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:16:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:16:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:17:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:17:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:17:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:17:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435507/SRX10435507.20_summits.bed INFO @ Tue, 02 Aug 2022 10:17:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (231 records, 4 fields): 19 millis CompletedMACS2peakCalling