Job ID = 10165887 SRX = SRX7879260 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: 00:06:44 29480730 reads; of these: 29480730 (100.00%) were unpaired; of these: 642589 (2.18%) aligned 0 times 24224195 (82.17%) aligned exactly 1 time 4613946 (15.65%) aligned >1 times 97.82% overall alignment rate Time searching: 00:06:44 Overall time: 00:06:44 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] 4411440 / 28838141 = 0.1530 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:20:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.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, 08 Oct 2020 20:20:01: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:20:01: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:20:05: 1000000 INFO @ Thu, 08 Oct 2020 20:20:10: 2000000 INFO @ Thu, 08 Oct 2020 20:20:15: 3000000 INFO @ Thu, 08 Oct 2020 20:20:20: 4000000 INFO @ Thu, 08 Oct 2020 20:20:25: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:20:30: 6000000 INFO @ Thu, 08 Oct 2020 20:20:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.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, 08 Oct 2020 20:20:31: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:20:31: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:20:35: 7000000 INFO @ Thu, 08 Oct 2020 20:20:36: 1000000 INFO @ Thu, 08 Oct 2020 20:20:40: 8000000 INFO @ Thu, 08 Oct 2020 20:20:41: 2000000 INFO @ Thu, 08 Oct 2020 20:20:45: 9000000 INFO @ Thu, 08 Oct 2020 20:20:46: 3000000 INFO @ Thu, 08 Oct 2020 20:20:50: 10000000 INFO @ Thu, 08 Oct 2020 20:20:51: 4000000 INFO @ Thu, 08 Oct 2020 20:20:55: 11000000 INFO @ Thu, 08 Oct 2020 20:20:56: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:21:00: 12000000 INFO @ Thu, 08 Oct 2020 20:21:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.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, 08 Oct 2020 20:21:01: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:21:01: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:21:01: 6000000 INFO @ Thu, 08 Oct 2020 20:21:05: 13000000 INFO @ Thu, 08 Oct 2020 20:21:06: 1000000 INFO @ Thu, 08 Oct 2020 20:21:07: 7000000 INFO @ Thu, 08 Oct 2020 20:21:11: 14000000 INFO @ Thu, 08 Oct 2020 20:21:11: 2000000 INFO @ Thu, 08 Oct 2020 20:21:12: 8000000 INFO @ Thu, 08 Oct 2020 20:21:16: 15000000 INFO @ Thu, 08 Oct 2020 20:21:16: 3000000 INFO @ Thu, 08 Oct 2020 20:21:17: 9000000 INFO @ Thu, 08 Oct 2020 20:21:21: 16000000 INFO @ Thu, 08 Oct 2020 20:21:22: 4000000 INFO @ Thu, 08 Oct 2020 20:21:22: 10000000 INFO @ Thu, 08 Oct 2020 20:21:26: 17000000 INFO @ Thu, 08 Oct 2020 20:21:27: 5000000 INFO @ Thu, 08 Oct 2020 20:21:27: 11000000 INFO @ Thu, 08 Oct 2020 20:21:31: 18000000 INFO @ Thu, 08 Oct 2020 20:21:32: 6000000 INFO @ Thu, 08 Oct 2020 20:21:33: 12000000 INFO @ Thu, 08 Oct 2020 20:21:37: 19000000 INFO @ Thu, 08 Oct 2020 20:21:37: 7000000 INFO @ Thu, 08 Oct 2020 20:21:38: 13000000 INFO @ Thu, 08 Oct 2020 20:21:42: 20000000 INFO @ Thu, 08 Oct 2020 20:21:43: 8000000 INFO @ Thu, 08 Oct 2020 20:21:43: 14000000 INFO @ Thu, 08 Oct 2020 20:21:47: 21000000 INFO @ Thu, 08 Oct 2020 20:21:48: 9000000 INFO @ Thu, 08 Oct 2020 20:21:49: 15000000 INFO @ Thu, 08 Oct 2020 20:21:52: 22000000 INFO @ Thu, 08 Oct 2020 20:21:53: 10000000 INFO @ Thu, 08 Oct 2020 20:21:54: 16000000 INFO @ Thu, 08 Oct 2020 20:21:58: 23000000 INFO @ Thu, 08 Oct 2020 20:21:59: 11000000 INFO @ Thu, 08 Oct 2020 20:21:59: 17000000 INFO @ Thu, 08 Oct 2020 20:22:03: 24000000 INFO @ Thu, 08 Oct 2020 20:22:04: 12000000 INFO @ Thu, 08 Oct 2020 20:22:04: 18000000 INFO @ Thu, 08 Oct 2020 20:22:05: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:22:05: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:22:05: #1 total tags in treatment: 24426701 INFO @ Thu, 08 Oct 2020 20:22:05: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:22:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:22:06: #1 tags after filtering in treatment: 24426701 INFO @ Thu, 08 Oct 2020 20:22:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:22:06: #1 finished! INFO @ Thu, 08 Oct 2020 20:22:06: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:22:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:22:07: #2 number of paired peaks: 148 WARNING @ Thu, 08 Oct 2020 20:22:07: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Thu, 08 Oct 2020 20:22:07: start model_add_line... INFO @ Thu, 08 Oct 2020 20:22:07: start X-correlation... INFO @ Thu, 08 Oct 2020 20:22:07: end of X-cor INFO @ Thu, 08 Oct 2020 20:22:07: #2 finished! INFO @ Thu, 08 Oct 2020 20:22:07: #2 predicted fragment length is 44 bps INFO @ Thu, 08 Oct 2020 20:22:07: #2 alternative fragment length(s) may be 1,44,500,557,590 bps INFO @ Thu, 08 Oct 2020 20:22:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.05_model.r WARNING @ Thu, 08 Oct 2020 20:22:07: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:22:07: #2 You may need to consider one of the other alternative d(s): 1,44,500,557,590 WARNING @ Thu, 08 Oct 2020 20:22:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:22:07: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:22:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:22:09: 13000000 INFO @ Thu, 08 Oct 2020 20:22:10: 19000000 INFO @ Thu, 08 Oct 2020 20:22:14: 14000000 INFO @ Thu, 08 Oct 2020 20:22:15: 20000000 INFO @ Thu, 08 Oct 2020 20:22:20: 15000000 INFO @ Thu, 08 Oct 2020 20:22:21: 21000000 INFO @ Thu, 08 Oct 2020 20:22:25: 16000000 INFO @ Thu, 08 Oct 2020 20:22:26: 22000000 INFO @ Thu, 08 Oct 2020 20:22:30: 17000000 INFO @ Thu, 08 Oct 2020 20:22:32: 23000000 INFO @ Thu, 08 Oct 2020 20:22:36: 18000000 INFO @ Thu, 08 Oct 2020 20:22:37: 24000000 INFO @ Thu, 08 Oct 2020 20:22:40: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:22:40: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:22:40: #1 total tags in treatment: 24426701 INFO @ Thu, 08 Oct 2020 20:22:40: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:22:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:22:40: #1 tags after filtering in treatment: 24426701 INFO @ Thu, 08 Oct 2020 20:22:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:22:40: #1 finished! INFO @ Thu, 08 Oct 2020 20:22:40: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:22:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:22:41: 19000000 INFO @ Thu, 08 Oct 2020 20:22:42: #2 number of paired peaks: 148 WARNING @ Thu, 08 Oct 2020 20:22:42: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Thu, 08 Oct 2020 20:22:42: start model_add_line... INFO @ Thu, 08 Oct 2020 20:22:42: start X-correlation... INFO @ Thu, 08 Oct 2020 20:22:42: end of X-cor INFO @ Thu, 08 Oct 2020 20:22:42: #2 finished! INFO @ Thu, 08 Oct 2020 20:22:42: #2 predicted fragment length is 44 bps INFO @ Thu, 08 Oct 2020 20:22:42: #2 alternative fragment length(s) may be 1,44,500,557,590 bps INFO @ Thu, 08 Oct 2020 20:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.10_model.r WARNING @ Thu, 08 Oct 2020 20:22:42: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:22:42: #2 You may need to consider one of the other alternative d(s): 1,44,500,557,590 WARNING @ Thu, 08 Oct 2020 20:22:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:22:42: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:22:42: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:22:46: 20000000 INFO @ Thu, 08 Oct 2020 20:22:48: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:22:52: 21000000 INFO @ Thu, 08 Oct 2020 20:22:57: 22000000 INFO @ Thu, 08 Oct 2020 20:23:02: 23000000 INFO @ Thu, 08 Oct 2020 20:23:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:23:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:23:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.05_summits.bed INFO @ Thu, 08 Oct 2020 20:23:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (750 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:23:07: 24000000 INFO @ Thu, 08 Oct 2020 20:23:09: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:23:09: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:23:09: #1 total tags in treatment: 24426701 INFO @ Thu, 08 Oct 2020 20:23:09: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:23:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:23:09: #1 tags after filtering in treatment: 24426701 INFO @ Thu, 08 Oct 2020 20:23:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:23:09: #1 finished! INFO @ Thu, 08 Oct 2020 20:23:09: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:23:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:23:11: #2 number of paired peaks: 148 WARNING @ Thu, 08 Oct 2020 20:23:11: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Thu, 08 Oct 2020 20:23:11: start model_add_line... INFO @ Thu, 08 Oct 2020 20:23:11: start X-correlation... INFO @ Thu, 08 Oct 2020 20:23:11: end of X-cor INFO @ Thu, 08 Oct 2020 20:23:11: #2 finished! INFO @ Thu, 08 Oct 2020 20:23:11: #2 predicted fragment length is 44 bps INFO @ Thu, 08 Oct 2020 20:23:11: #2 alternative fragment length(s) may be 1,44,500,557,590 bps INFO @ Thu, 08 Oct 2020 20:23:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.20_model.r WARNING @ Thu, 08 Oct 2020 20:23:11: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:23:11: #2 You may need to consider one of the other alternative d(s): 1,44,500,557,590 WARNING @ Thu, 08 Oct 2020 20:23:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:23:11: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:23:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:23:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:23:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:23:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:23:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.10_summits.bed INFO @ Thu, 08 Oct 2020 20:23:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (446 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:23:52: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:24:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:24:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7879260/SRX7879260.20_summits.bed INFO @ Thu, 08 Oct 2020 20:24:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (134 records, 4 fields): 2 millis CompletedMACS2peakCalling