Job ID = 10165943 SRX = SRX8331143 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: 00:08:48 26926268 reads; of these: 26926268 (100.00%) were unpaired; of these: 915898 (3.40%) aligned 0 times 22007283 (81.73%) aligned exactly 1 time 4003087 (14.87%) aligned >1 times 96.60% overall alignment rate Time searching: 00:08:48 Overall time: 00:08:48 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] 11043652 / 26010370 = 0.4246 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 20:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.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 20:29:56: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:29:56: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:30:02: 1000000 INFO @ Thu, 08 Oct 2020 20:30:07: 2000000 INFO @ Thu, 08 Oct 2020 20:30:13: 3000000 INFO @ Thu, 08 Oct 2020 20:30:18: 4000000 INFO @ Thu, 08 Oct 2020 20:30:24: 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 20:30:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.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 20:30:26: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:30:26: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:30:30: 6000000 INFO @ Thu, 08 Oct 2020 20:30:32: 1000000 INFO @ Thu, 08 Oct 2020 20:30:36: 7000000 INFO @ Thu, 08 Oct 2020 20:30:39: 2000000 INFO @ Thu, 08 Oct 2020 20:30:42: 8000000 INFO @ Thu, 08 Oct 2020 20:30:45: 3000000 INFO @ Thu, 08 Oct 2020 20:30:49: 9000000 INFO @ Thu, 08 Oct 2020 20:30:51: 4000000 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 20:30:55: 10000000 INFO @ Thu, 08 Oct 2020 20:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.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 20:30:56: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:30:56: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:30:57: 5000000 INFO @ Thu, 08 Oct 2020 20:31:01: 11000000 INFO @ Thu, 08 Oct 2020 20:31:02: 1000000 INFO @ Thu, 08 Oct 2020 20:31:03: 6000000 INFO @ Thu, 08 Oct 2020 20:31:07: 12000000 INFO @ Thu, 08 Oct 2020 20:31:09: 2000000 INFO @ Thu, 08 Oct 2020 20:31:09: 7000000 INFO @ Thu, 08 Oct 2020 20:31:13: 13000000 INFO @ Thu, 08 Oct 2020 20:31:15: 3000000 INFO @ Thu, 08 Oct 2020 20:31:16: 8000000 INFO @ Thu, 08 Oct 2020 20:31:20: 14000000 INFO @ Thu, 08 Oct 2020 20:31:21: 4000000 INFO @ Thu, 08 Oct 2020 20:31:22: 9000000 INFO @ Thu, 08 Oct 2020 20:31:26: #1 tag size is determined as 74 bps INFO @ Thu, 08 Oct 2020 20:31:26: #1 tag size = 74 INFO @ Thu, 08 Oct 2020 20:31:26: #1 total tags in treatment: 14966718 INFO @ Thu, 08 Oct 2020 20:31:26: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:31:26: #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 20:31:26: #1 tags after filtering in treatment: 14966718 INFO @ Thu, 08 Oct 2020 20:31:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:31:26: #1 finished! INFO @ Thu, 08 Oct 2020 20:31:26: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:31:27: #2 number of paired peaks: 289 WARNING @ Thu, 08 Oct 2020 20:31:27: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Thu, 08 Oct 2020 20:31:27: start model_add_line... INFO @ Thu, 08 Oct 2020 20:31:27: start X-correlation... INFO @ Thu, 08 Oct 2020 20:31:27: end of X-cor INFO @ Thu, 08 Oct 2020 20:31:27: #2 finished! INFO @ Thu, 08 Oct 2020 20:31:27: #2 predicted fragment length is 58 bps INFO @ Thu, 08 Oct 2020 20:31:27: #2 alternative fragment length(s) may be 2,58,573 bps INFO @ Thu, 08 Oct 2020 20:31:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.05_model.r WARNING @ Thu, 08 Oct 2020 20:31:27: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:31:27: #2 You may need to consider one of the other alternative d(s): 2,58,573 WARNING @ Thu, 08 Oct 2020 20:31:27: #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 20:31:27: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:31:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:31:27: 5000000 INFO @ Thu, 08 Oct 2020 20:31:28: 10000000 INFO @ Thu, 08 Oct 2020 20:31:33: 6000000 INFO @ Thu, 08 Oct 2020 20:31:34: 11000000 INFO @ Thu, 08 Oct 2020 20:31:39: 7000000 INFO @ Thu, 08 Oct 2020 20:31:41: 12000000 INFO @ Thu, 08 Oct 2020 20:31:46: 8000000 INFO @ Thu, 08 Oct 2020 20:31:47: 13000000 INFO @ Thu, 08 Oct 2020 20:31:52: 9000000 INFO @ Thu, 08 Oct 2020 20:31:53: 14000000 INFO @ Thu, 08 Oct 2020 20:31:55: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:31:58: 10000000 INFO @ Thu, 08 Oct 2020 20:31:59: #1 tag size is determined as 74 bps INFO @ Thu, 08 Oct 2020 20:31:59: #1 tag size = 74 INFO @ Thu, 08 Oct 2020 20:31:59: #1 total tags in treatment: 14966718 INFO @ Thu, 08 Oct 2020 20:31:59: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:31:59: #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 20:31:59: #1 tags after filtering in treatment: 14966718 INFO @ Thu, 08 Oct 2020 20:31:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:31:59: #1 finished! INFO @ Thu, 08 Oct 2020 20:31:59: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:31:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:32:00: #2 number of paired peaks: 289 WARNING @ Thu, 08 Oct 2020 20:32:00: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Thu, 08 Oct 2020 20:32:00: start model_add_line... INFO @ Thu, 08 Oct 2020 20:32:00: start X-correlation... INFO @ Thu, 08 Oct 2020 20:32:00: end of X-cor INFO @ Thu, 08 Oct 2020 20:32:00: #2 finished! INFO @ Thu, 08 Oct 2020 20:32:00: #2 predicted fragment length is 58 bps INFO @ Thu, 08 Oct 2020 20:32:00: #2 alternative fragment length(s) may be 2,58,573 bps INFO @ Thu, 08 Oct 2020 20:32:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.10_model.r WARNING @ Thu, 08 Oct 2020 20:32:00: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:32:00: #2 You may need to consider one of the other alternative d(s): 2,58,573 WARNING @ Thu, 08 Oct 2020 20:32:00: #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 20:32:00: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:32:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:32:04: 11000000 INFO @ Thu, 08 Oct 2020 20:32:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:32:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:32:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.05_summits.bed INFO @ Thu, 08 Oct 2020 20:32:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (671 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:32:10: 12000000 INFO @ Thu, 08 Oct 2020 20:32:16: 13000000 INFO @ Thu, 08 Oct 2020 20:32:21: 14000000 INFO @ Thu, 08 Oct 2020 20:32:27: #1 tag size is determined as 74 bps INFO @ Thu, 08 Oct 2020 20:32:27: #1 tag size = 74 INFO @ Thu, 08 Oct 2020 20:32:27: #1 total tags in treatment: 14966718 INFO @ Thu, 08 Oct 2020 20:32:27: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:32:27: #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 20:32:27: #1 tags after filtering in treatment: 14966718 INFO @ Thu, 08 Oct 2020 20:32:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:32:27: #1 finished! INFO @ Thu, 08 Oct 2020 20:32:27: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:32:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:32:28: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:32:28: #2 number of paired peaks: 289 WARNING @ Thu, 08 Oct 2020 20:32:28: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Thu, 08 Oct 2020 20:32:28: start model_add_line... INFO @ Thu, 08 Oct 2020 20:32:28: start X-correlation... INFO @ Thu, 08 Oct 2020 20:32:28: end of X-cor INFO @ Thu, 08 Oct 2020 20:32:28: #2 finished! INFO @ Thu, 08 Oct 2020 20:32:28: #2 predicted fragment length is 58 bps INFO @ Thu, 08 Oct 2020 20:32:28: #2 alternative fragment length(s) may be 2,58,573 bps INFO @ Thu, 08 Oct 2020 20:32:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.20_model.r WARNING @ Thu, 08 Oct 2020 20:32:28: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:32:28: #2 You may need to consider one of the other alternative d(s): 2,58,573 WARNING @ Thu, 08 Oct 2020 20:32:28: #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 20:32:28: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:32:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:32:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:32:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:32:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.10_summits.bed INFO @ Thu, 08 Oct 2020 20:32:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (455 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:32:56: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:33:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:33:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:33:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331143/SRX8331143.20_summits.bed INFO @ Thu, 08 Oct 2020 20:33:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (209 records, 4 fields): 2 millis CompletedMACS2peakCalling