Job ID = 16434868 SRX = SRX11633404 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: 00:05:37 17038881 reads; of these: 17038881 (100.00%) were unpaired; of these: 1113230 (6.53%) aligned 0 times 13623558 (79.96%) aligned exactly 1 time 2302093 (13.51%) aligned >1 times 93.47% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 2654125 / 15925651 = 0.1667 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 10:18:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.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 10:18:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:18:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:18:29: 1000000 INFO @ Tue, 02 Aug 2022 10:18:36: 2000000 INFO @ Tue, 02 Aug 2022 10:18:43: 3000000 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 10:18:51: 4000000 INFO @ Tue, 02 Aug 2022 10:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.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 10:18:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:18:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:18:58: 5000000 INFO @ Tue, 02 Aug 2022 10:19:00: 1000000 INFO @ Tue, 02 Aug 2022 10:19:07: 6000000 INFO @ Tue, 02 Aug 2022 10:19:08: 2000000 INFO @ Tue, 02 Aug 2022 10:19:15: 7000000 INFO @ Tue, 02 Aug 2022 10:19:16: 3000000 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 10:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.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 10:19:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:19:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:19:23: 8000000 INFO @ Tue, 02 Aug 2022 10:19:25: 4000000 INFO @ Tue, 02 Aug 2022 10:19:30: 1000000 INFO @ Tue, 02 Aug 2022 10:19:31: 9000000 INFO @ Tue, 02 Aug 2022 10:19:33: 5000000 INFO @ Tue, 02 Aug 2022 10:19:38: 2000000 INFO @ Tue, 02 Aug 2022 10:19:40: 10000000 INFO @ Tue, 02 Aug 2022 10:19:41: 6000000 INFO @ Tue, 02 Aug 2022 10:19:46: 3000000 INFO @ Tue, 02 Aug 2022 10:19:48: 11000000 INFO @ Tue, 02 Aug 2022 10:19:49: 7000000 INFO @ Tue, 02 Aug 2022 10:19:54: 4000000 INFO @ Tue, 02 Aug 2022 10:19:57: 8000000 INFO @ Tue, 02 Aug 2022 10:19:57: 12000000 INFO @ Tue, 02 Aug 2022 10:20:03: 5000000 INFO @ Tue, 02 Aug 2022 10:20:04: 9000000 INFO @ Tue, 02 Aug 2022 10:20:05: 13000000 INFO @ Tue, 02 Aug 2022 10:20:08: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:20:08: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:20:08: #1 total tags in treatment: 13271526 INFO @ Tue, 02 Aug 2022 10:20:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:20:08: #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 10:20:08: #1 tags after filtering in treatment: 13271526 INFO @ Tue, 02 Aug 2022 10:20:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:20:08: #1 finished! INFO @ Tue, 02 Aug 2022 10:20:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:20:09: #2 number of paired peaks: 240 WARNING @ Tue, 02 Aug 2022 10:20:09: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Tue, 02 Aug 2022 10:20:09: start model_add_line... INFO @ Tue, 02 Aug 2022 10:20:09: start X-correlation... INFO @ Tue, 02 Aug 2022 10:20:09: end of X-cor INFO @ Tue, 02 Aug 2022 10:20:09: #2 finished! INFO @ Tue, 02 Aug 2022 10:20:09: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 10:20:09: #2 alternative fragment length(s) may be 3,63,564 bps INFO @ Tue, 02 Aug 2022 10:20:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.05_model.r WARNING @ Tue, 02 Aug 2022 10:20:09: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:20:09: #2 You may need to consider one of the other alternative d(s): 3,63,564 WARNING @ Tue, 02 Aug 2022 10:20:09: #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 10:20:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:20:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:20:11: 6000000 INFO @ Tue, 02 Aug 2022 10:20:12: 10000000 INFO @ Tue, 02 Aug 2022 10:20:18: 7000000 INFO @ Tue, 02 Aug 2022 10:20:20: 11000000 INFO @ Tue, 02 Aug 2022 10:20:26: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:20:27: 12000000 INFO @ Tue, 02 Aug 2022 10:20:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:20:33: 9000000 INFO @ Tue, 02 Aug 2022 10:20:34: 13000000 INFO @ Tue, 02 Aug 2022 10:20:36: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:20:36: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:20:36: #1 total tags in treatment: 13271526 INFO @ Tue, 02 Aug 2022 10:20:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:20:36: #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 10:20:36: #1 tags after filtering in treatment: 13271526 INFO @ Tue, 02 Aug 2022 10:20:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:20:36: #1 finished! INFO @ Tue, 02 Aug 2022 10:20:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:20:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:20:37: #2 number of paired peaks: 240 WARNING @ Tue, 02 Aug 2022 10:20:37: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Tue, 02 Aug 2022 10:20:37: start model_add_line... INFO @ Tue, 02 Aug 2022 10:20:37: start X-correlation... INFO @ Tue, 02 Aug 2022 10:20:38: end of X-cor INFO @ Tue, 02 Aug 2022 10:20:38: #2 finished! INFO @ Tue, 02 Aug 2022 10:20:38: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 10:20:38: #2 alternative fragment length(s) may be 3,63,564 bps INFO @ Tue, 02 Aug 2022 10:20:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.10_model.r WARNING @ Tue, 02 Aug 2022 10:20:38: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:20:38: #2 You may need to consider one of the other alternative d(s): 3,63,564 WARNING @ Tue, 02 Aug 2022 10:20:38: #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 10:20:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:20:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:20:40: 10000000 INFO @ Tue, 02 Aug 2022 10:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.05_summits.bed INFO @ Tue, 02 Aug 2022 10:20:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (539 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:20:47: 11000000 INFO @ Tue, 02 Aug 2022 10:20:53: 12000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:21:00: 13000000 INFO @ Tue, 02 Aug 2022 10:21:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:21:01: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:21:01: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:21:01: #1 total tags in treatment: 13271526 INFO @ Tue, 02 Aug 2022 10:21:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:21:01: #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 10:21:02: #1 tags after filtering in treatment: 13271526 INFO @ Tue, 02 Aug 2022 10:21:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:21:02: #1 finished! INFO @ Tue, 02 Aug 2022 10:21:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:21:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:21:03: #2 number of paired peaks: 240 WARNING @ Tue, 02 Aug 2022 10:21:03: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Tue, 02 Aug 2022 10:21:03: start model_add_line... INFO @ Tue, 02 Aug 2022 10:21:03: start X-correlation... INFO @ Tue, 02 Aug 2022 10:21:03: end of X-cor INFO @ Tue, 02 Aug 2022 10:21:03: #2 finished! INFO @ Tue, 02 Aug 2022 10:21:03: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 10:21:03: #2 alternative fragment length(s) may be 3,63,564 bps INFO @ Tue, 02 Aug 2022 10:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.20_model.r WARNING @ Tue, 02 Aug 2022 10:21:03: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:21:03: #2 You may need to consider one of the other alternative d(s): 3,63,564 WARNING @ Tue, 02 Aug 2022 10:21:03: #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 10:21:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:21:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.10_summits.bed INFO @ Tue, 02 Aug 2022 10:21:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (375 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:21:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:21:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:21:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:21:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11633404/SRX11633404.20_summits.bed INFO @ Tue, 02 Aug 2022 10:21:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (177 records, 4 fields): 18 millis CompletedMACS2peakCalling