Job ID = 14158778 SRX = SRX7739525 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:26 23722090 reads; of these: 23722090 (100.00%) were unpaired; of these: 1057199 (4.46%) aligned 0 times 18865151 (79.53%) aligned exactly 1 time 3799740 (16.02%) aligned >1 times 95.54% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 2480803 / 22664891 = 0.1095 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 18:00:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.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 18:00:24: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:00:24: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:00:31: 1000000 INFO @ Wed, 08 Dec 2021 18:00:37: 2000000 INFO @ Wed, 08 Dec 2021 18:00:43: 3000000 INFO @ Wed, 08 Dec 2021 18:00:50: 4000000 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 18:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.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 18:00:54: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:00:54: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:00:56: 5000000 INFO @ Wed, 08 Dec 2021 18:01:01: 1000000 INFO @ Wed, 08 Dec 2021 18:01:03: 6000000 INFO @ Wed, 08 Dec 2021 18:01:07: 2000000 INFO @ Wed, 08 Dec 2021 18:01:10: 7000000 INFO @ Wed, 08 Dec 2021 18:01:14: 3000000 INFO @ Wed, 08 Dec 2021 18:01:17: 8000000 INFO @ Wed, 08 Dec 2021 18:01:20: 4000000 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 18:01:24: 9000000 INFO @ Wed, 08 Dec 2021 18:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.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 18:01:24: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:01:24: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:01:27: 5000000 INFO @ Wed, 08 Dec 2021 18:01:31: 10000000 INFO @ Wed, 08 Dec 2021 18:01:31: 1000000 INFO @ Wed, 08 Dec 2021 18:01:33: 6000000 INFO @ Wed, 08 Dec 2021 18:01:37: 11000000 INFO @ Wed, 08 Dec 2021 18:01:38: 2000000 INFO @ Wed, 08 Dec 2021 18:01:40: 7000000 INFO @ Wed, 08 Dec 2021 18:01:44: 3000000 INFO @ Wed, 08 Dec 2021 18:01:44: 12000000 INFO @ Wed, 08 Dec 2021 18:01:47: 8000000 INFO @ Wed, 08 Dec 2021 18:01:51: 4000000 INFO @ Wed, 08 Dec 2021 18:01:51: 13000000 INFO @ Wed, 08 Dec 2021 18:01:53: 9000000 INFO @ Wed, 08 Dec 2021 18:01:57: 5000000 INFO @ Wed, 08 Dec 2021 18:01:58: 14000000 INFO @ Wed, 08 Dec 2021 18:02:00: 10000000 INFO @ Wed, 08 Dec 2021 18:02:04: 6000000 INFO @ Wed, 08 Dec 2021 18:02:05: 15000000 INFO @ Wed, 08 Dec 2021 18:02:06: 11000000 INFO @ Wed, 08 Dec 2021 18:02:11: 7000000 INFO @ Wed, 08 Dec 2021 18:02:12: 16000000 INFO @ Wed, 08 Dec 2021 18:02:13: 12000000 INFO @ Wed, 08 Dec 2021 18:02:17: 8000000 INFO @ Wed, 08 Dec 2021 18:02:19: 17000000 INFO @ Wed, 08 Dec 2021 18:02:19: 13000000 INFO @ Wed, 08 Dec 2021 18:02:24: 9000000 INFO @ Wed, 08 Dec 2021 18:02:26: 14000000 INFO @ Wed, 08 Dec 2021 18:02:26: 18000000 INFO @ Wed, 08 Dec 2021 18:02:30: 10000000 INFO @ Wed, 08 Dec 2021 18:02:32: 15000000 INFO @ Wed, 08 Dec 2021 18:02:33: 19000000 INFO @ Wed, 08 Dec 2021 18:02:37: 11000000 INFO @ Wed, 08 Dec 2021 18:02:39: 16000000 INFO @ Wed, 08 Dec 2021 18:02:40: 20000000 INFO @ Wed, 08 Dec 2021 18:02:41: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:02:41: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:02:41: #1 total tags in treatment: 20184088 INFO @ Wed, 08 Dec 2021 18:02:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:02:41: #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 18:02:41: #1 tags after filtering in treatment: 20184088 INFO @ Wed, 08 Dec 2021 18:02:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:02:41: #1 finished! INFO @ Wed, 08 Dec 2021 18:02:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:02:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:02:42: #2 number of paired peaks: 208 WARNING @ Wed, 08 Dec 2021 18:02:42: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Wed, 08 Dec 2021 18:02:42: start model_add_line... INFO @ Wed, 08 Dec 2021 18:02:43: start X-correlation... INFO @ Wed, 08 Dec 2021 18:02:43: end of X-cor INFO @ Wed, 08 Dec 2021 18:02:43: #2 finished! INFO @ Wed, 08 Dec 2021 18:02:43: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 18:02:43: #2 alternative fragment length(s) may be 1,15,45,499,558,576,597 bps INFO @ Wed, 08 Dec 2021 18:02:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.05_model.r WARNING @ Wed, 08 Dec 2021 18:02:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:02:43: #2 You may need to consider one of the other alternative d(s): 1,15,45,499,558,576,597 WARNING @ Wed, 08 Dec 2021 18:02:43: #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 18:02:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:02:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:02:43: 12000000 INFO @ Wed, 08 Dec 2021 18:02:45: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:02:49: 13000000 INFO @ Wed, 08 Dec 2021 18:02:51: 18000000 INFO @ Wed, 08 Dec 2021 18:02:55: 14000000 INFO @ Wed, 08 Dec 2021 18:02:57: 19000000 INFO @ Wed, 08 Dec 2021 18:03:01: 15000000 INFO @ Wed, 08 Dec 2021 18:03:03: 20000000 INFO @ Wed, 08 Dec 2021 18:03:05: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:03:05: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:03:05: #1 total tags in treatment: 20184088 INFO @ Wed, 08 Dec 2021 18:03:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:03:05: #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 18:03:05: #1 tags after filtering in treatment: 20184088 INFO @ Wed, 08 Dec 2021 18:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:03:05: #1 finished! INFO @ Wed, 08 Dec 2021 18:03:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:03:06: #2 number of paired peaks: 208 WARNING @ Wed, 08 Dec 2021 18:03:06: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Wed, 08 Dec 2021 18:03:06: start model_add_line... INFO @ Wed, 08 Dec 2021 18:03:06: start X-correlation... INFO @ Wed, 08 Dec 2021 18:03:06: end of X-cor INFO @ Wed, 08 Dec 2021 18:03:06: #2 finished! INFO @ Wed, 08 Dec 2021 18:03:06: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 18:03:06: #2 alternative fragment length(s) may be 1,15,45,499,558,576,597 bps INFO @ Wed, 08 Dec 2021 18:03:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.10_model.r WARNING @ Wed, 08 Dec 2021 18:03:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:03:06: #2 You may need to consider one of the other alternative d(s): 1,15,45,499,558,576,597 WARNING @ Wed, 08 Dec 2021 18:03:06: #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 18:03:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:03:07: 16000000 INFO @ Wed, 08 Dec 2021 18:03:13: 17000000 INFO @ Wed, 08 Dec 2021 18:03:14: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:03:19: 18000000 INFO @ Wed, 08 Dec 2021 18:03:24: 19000000 INFO @ Wed, 08 Dec 2021 18:03:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:03:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:03:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.05_summits.bed INFO @ Wed, 08 Dec 2021 18:03:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:03:30: 20000000 INFO @ Wed, 08 Dec 2021 18:03:31: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:03:31: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:03:31: #1 total tags in treatment: 20184088 INFO @ Wed, 08 Dec 2021 18:03:31: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:03:31: #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 18:03:31: #1 tags after filtering in treatment: 20184088 INFO @ Wed, 08 Dec 2021 18:03:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:03:31: #1 finished! INFO @ Wed, 08 Dec 2021 18:03:31: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:03:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:03:33: #2 number of paired peaks: 208 WARNING @ Wed, 08 Dec 2021 18:03:33: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Wed, 08 Dec 2021 18:03:33: start model_add_line... INFO @ Wed, 08 Dec 2021 18:03:33: start X-correlation... INFO @ Wed, 08 Dec 2021 18:03:33: end of X-cor INFO @ Wed, 08 Dec 2021 18:03:33: #2 finished! INFO @ Wed, 08 Dec 2021 18:03:33: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 18:03:33: #2 alternative fragment length(s) may be 1,15,45,499,558,576,597 bps INFO @ Wed, 08 Dec 2021 18:03:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.20_model.r WARNING @ Wed, 08 Dec 2021 18:03:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:03:33: #2 You may need to consider one of the other alternative d(s): 1,15,45,499,558,576,597 WARNING @ Wed, 08 Dec 2021 18:03:33: #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 18:03:33: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:03:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:03:36: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:03:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:03:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:03:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.10_summits.bed INFO @ Wed, 08 Dec 2021 18:03:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:04:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:04:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:04:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:04:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7739525/SRX7739525.20_summits.bed INFO @ Wed, 08 Dec 2021 18:04:18: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling