Job ID = 14160518 SRX = SRX8151888 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 22302645 reads; of these: 22302645 (100.00%) were unpaired; of these: 1672503 (7.50%) aligned 0 times 17208707 (77.16%) aligned exactly 1 time 3421435 (15.34%) aligned >1 times 92.50% 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 12 files... [bam_rmdupse_core] 1965354 / 20630142 = 0.0953 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 @ Thu, 09 Dec 2021 03:05:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.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 @ Thu, 09 Dec 2021 03:05:00: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:05:00: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:05:05: 1000000 INFO @ Thu, 09 Dec 2021 03:05:10: 2000000 INFO @ Thu, 09 Dec 2021 03:05:14: 3000000 INFO @ Thu, 09 Dec 2021 03:05:19: 4000000 INFO @ Thu, 09 Dec 2021 03:05:24: 5000000 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 @ Thu, 09 Dec 2021 03:05:29: 6000000 INFO @ Thu, 09 Dec 2021 03:05:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.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 @ Thu, 09 Dec 2021 03:05:30: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:05:30: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:05:34: 7000000 INFO @ Thu, 09 Dec 2021 03:05:35: 1000000 INFO @ Thu, 09 Dec 2021 03:05:39: 8000000 INFO @ Thu, 09 Dec 2021 03:05:40: 2000000 INFO @ Thu, 09 Dec 2021 03:05:44: 9000000 INFO @ Thu, 09 Dec 2021 03:05:45: 3000000 INFO @ Thu, 09 Dec 2021 03:05:50: 10000000 INFO @ Thu, 09 Dec 2021 03:05:51: 4000000 INFO @ Thu, 09 Dec 2021 03:05:55: 11000000 INFO @ Thu, 09 Dec 2021 03:05:56: 5000000 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 @ Thu, 09 Dec 2021 03:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.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 @ Thu, 09 Dec 2021 03:06:00: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:06:00: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:06:00: 12000000 INFO @ Thu, 09 Dec 2021 03:06:01: 6000000 INFO @ Thu, 09 Dec 2021 03:06:05: 1000000 INFO @ Thu, 09 Dec 2021 03:06:05: 13000000 INFO @ Thu, 09 Dec 2021 03:06:06: 7000000 INFO @ Thu, 09 Dec 2021 03:06:10: 14000000 INFO @ Thu, 09 Dec 2021 03:06:10: 2000000 INFO @ Thu, 09 Dec 2021 03:06:11: 8000000 INFO @ Thu, 09 Dec 2021 03:06:16: 15000000 INFO @ Thu, 09 Dec 2021 03:06:16: 3000000 INFO @ Thu, 09 Dec 2021 03:06:16: 9000000 INFO @ Thu, 09 Dec 2021 03:06:21: 16000000 INFO @ Thu, 09 Dec 2021 03:06:21: 4000000 INFO @ Thu, 09 Dec 2021 03:06:22: 10000000 INFO @ Thu, 09 Dec 2021 03:06:26: 17000000 INFO @ Thu, 09 Dec 2021 03:06:26: 5000000 INFO @ Thu, 09 Dec 2021 03:06:27: 11000000 INFO @ Thu, 09 Dec 2021 03:06:31: 18000000 INFO @ Thu, 09 Dec 2021 03:06:31: 6000000 INFO @ Thu, 09 Dec 2021 03:06:32: 12000000 INFO @ Thu, 09 Dec 2021 03:06:34: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:06:34: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:06:34: #1 total tags in treatment: 18664788 INFO @ Thu, 09 Dec 2021 03:06:34: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:06:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:06:35: #1 tags after filtering in treatment: 18664788 INFO @ Thu, 09 Dec 2021 03:06:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:06:35: #1 finished! INFO @ Thu, 09 Dec 2021 03:06:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:06:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:06:36: #2 number of paired peaks: 197 WARNING @ Thu, 09 Dec 2021 03:06:36: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Thu, 09 Dec 2021 03:06:36: start model_add_line... INFO @ Thu, 09 Dec 2021 03:06:36: start X-correlation... INFO @ Thu, 09 Dec 2021 03:06:36: end of X-cor INFO @ Thu, 09 Dec 2021 03:06:36: #2 finished! INFO @ Thu, 09 Dec 2021 03:06:36: #2 predicted fragment length is 2 bps INFO @ Thu, 09 Dec 2021 03:06:36: #2 alternative fragment length(s) may be 2,12,39,569,592 bps INFO @ Thu, 09 Dec 2021 03:06:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.05_model.r WARNING @ Thu, 09 Dec 2021 03:06:36: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:06:36: #2 You may need to consider one of the other alternative d(s): 2,12,39,569,592 WARNING @ Thu, 09 Dec 2021 03:06:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:06:36: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:06:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:06:36: 7000000 INFO @ Thu, 09 Dec 2021 03:06:37: 13000000 INFO @ Thu, 09 Dec 2021 03:06:42: 8000000 INFO @ Thu, 09 Dec 2021 03:06:42: 14000000 INFO @ Thu, 09 Dec 2021 03:06:47: 9000000 INFO @ Thu, 09 Dec 2021 03:06:47: 15000000 INFO @ Thu, 09 Dec 2021 03:06:52: 10000000 INFO @ Thu, 09 Dec 2021 03:06:53: 16000000 INFO @ Thu, 09 Dec 2021 03:06:57: 11000000 INFO @ Thu, 09 Dec 2021 03:06:58: 17000000 INFO @ Thu, 09 Dec 2021 03:07:02: 12000000 INFO @ Thu, 09 Dec 2021 03:07:03: 18000000 INFO @ Thu, 09 Dec 2021 03:07:04: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:07:06: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:07:06: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:07:06: #1 total tags in treatment: 18664788 INFO @ Thu, 09 Dec 2021 03:07:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:07:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:07:06: #1 tags after filtering in treatment: 18664788 INFO @ Thu, 09 Dec 2021 03:07:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:07:06: #1 finished! INFO @ Thu, 09 Dec 2021 03:07:06: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:07:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:07:07: 13000000 INFO @ Thu, 09 Dec 2021 03:07:08: #2 number of paired peaks: 197 WARNING @ Thu, 09 Dec 2021 03:07:08: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Thu, 09 Dec 2021 03:07:08: start model_add_line... INFO @ Thu, 09 Dec 2021 03:07:08: start X-correlation... INFO @ Thu, 09 Dec 2021 03:07:08: end of X-cor INFO @ Thu, 09 Dec 2021 03:07:08: #2 finished! INFO @ Thu, 09 Dec 2021 03:07:08: #2 predicted fragment length is 2 bps INFO @ Thu, 09 Dec 2021 03:07:08: #2 alternative fragment length(s) may be 2,12,39,569,592 bps INFO @ Thu, 09 Dec 2021 03:07:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.10_model.r WARNING @ Thu, 09 Dec 2021 03:07:08: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:07:08: #2 You may need to consider one of the other alternative d(s): 2,12,39,569,592 WARNING @ Thu, 09 Dec 2021 03:07:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:07:08: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:07:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:07:12: 14000000 INFO @ Thu, 09 Dec 2021 03:07:17: 15000000 INFO @ Thu, 09 Dec 2021 03:07:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.05_summits.bed INFO @ Thu, 09 Dec 2021 03:07:19: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:07:22: 16000000 INFO @ Thu, 09 Dec 2021 03:07:27: 17000000 INFO @ Thu, 09 Dec 2021 03:07:32: 18000000 INFO @ Thu, 09 Dec 2021 03:07:36: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:07:36: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:07:36: #1 total tags in treatment: 18664788 INFO @ Thu, 09 Dec 2021 03:07:36: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:07:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:07:36: #1 tags after filtering in treatment: 18664788 INFO @ Thu, 09 Dec 2021 03:07:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:07:36: #1 finished! INFO @ Thu, 09 Dec 2021 03:07:36: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:07:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:07:37: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:07:37: #2 number of paired peaks: 197 WARNING @ Thu, 09 Dec 2021 03:07:37: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Thu, 09 Dec 2021 03:07:37: start model_add_line... INFO @ Thu, 09 Dec 2021 03:07:37: start X-correlation... INFO @ Thu, 09 Dec 2021 03:07:37: end of X-cor INFO @ Thu, 09 Dec 2021 03:07:37: #2 finished! INFO @ Thu, 09 Dec 2021 03:07:37: #2 predicted fragment length is 2 bps INFO @ Thu, 09 Dec 2021 03:07:37: #2 alternative fragment length(s) may be 2,12,39,569,592 bps INFO @ Thu, 09 Dec 2021 03:07:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.20_model.r WARNING @ Thu, 09 Dec 2021 03:07:37: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:07:37: #2 You may need to consider one of the other alternative d(s): 2,12,39,569,592 WARNING @ Thu, 09 Dec 2021 03:07:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:07:37: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:07:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:07:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:07:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:07:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.10_summits.bed INFO @ Thu, 09 Dec 2021 03:07:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:08:06: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:08:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:08:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:08:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8151888/SRX8151888.20_summits.bed INFO @ Thu, 09 Dec 2021 03:08:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling