Job ID = 6455715 SRX = SRX288012 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:15:21 prefetch.2.10.7: 1) Downloading 'SRR870201'... 2020-06-21T10:15:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:42 prefetch.2.10.7: 1) 'SRR870201' was downloaded successfully Read 18022423 spots for SRR870201/SRR870201.sra Written 18022423 spots for SRR870201/SRR870201.sra 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: 00:04:47 18022423 reads; of these: 18022423 (100.00%) were unpaired; of these: 1505201 (8.35%) aligned 0 times 12417401 (68.90%) aligned exactly 1 time 4099821 (22.75%) aligned >1 times 91.65% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2374823 / 16517222 = 0.1438 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 @ Sun, 21 Jun 2020 19:29:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 19:29:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:57: 1000000 INFO @ Sun, 21 Jun 2020 19:30:03: 2000000 INFO @ Sun, 21 Jun 2020 19:30:09: 3000000 INFO @ Sun, 21 Jun 2020 19:30:15: 4000000 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 @ Sun, 21 Jun 2020 19:30:20: 5000000 INFO @ Sun, 21 Jun 2020 19:30:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 19:30:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:26: 6000000 INFO @ Sun, 21 Jun 2020 19:30:27: 1000000 INFO @ Sun, 21 Jun 2020 19:30:32: 2000000 INFO @ Sun, 21 Jun 2020 19:30:32: 7000000 INFO @ Sun, 21 Jun 2020 19:30:37: 3000000 INFO @ Sun, 21 Jun 2020 19:30:38: 8000000 INFO @ Sun, 21 Jun 2020 19:30:42: 4000000 INFO @ Sun, 21 Jun 2020 19:30:44: 9000000 INFO @ Sun, 21 Jun 2020 19:30:47: 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 @ Sun, 21 Jun 2020 19:30:50: 10000000 INFO @ Sun, 21 Jun 2020 19:30:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 19:30:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:53: 6000000 INFO @ Sun, 21 Jun 2020 19:30:56: 11000000 INFO @ Sun, 21 Jun 2020 19:30:57: 1000000 INFO @ Sun, 21 Jun 2020 19:30:58: 7000000 INFO @ Sun, 21 Jun 2020 19:31:02: 2000000 INFO @ Sun, 21 Jun 2020 19:31:02: 12000000 INFO @ Sun, 21 Jun 2020 19:31:03: 8000000 INFO @ Sun, 21 Jun 2020 19:31:07: 3000000 INFO @ Sun, 21 Jun 2020 19:31:08: 13000000 INFO @ Sun, 21 Jun 2020 19:31:08: 9000000 INFO @ Sun, 21 Jun 2020 19:31:12: 4000000 INFO @ Sun, 21 Jun 2020 19:31:13: 10000000 INFO @ Sun, 21 Jun 2020 19:31:14: 14000000 INFO @ Sun, 21 Jun 2020 19:31:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:15: #1 total tags in treatment: 14142399 INFO @ Sun, 21 Jun 2020 19:31:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:31:15: #1 tags after filtering in treatment: 14142399 INFO @ Sun, 21 Jun 2020 19:31:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:16: #2 number of paired peaks: 340 WARNING @ Sun, 21 Jun 2020 19:31:16: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:16: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:31:16: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:31:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.05_model.r WARNING @ Sun, 21 Jun 2020 19:31:16: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:31:16: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:31:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:31:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:17: 5000000 INFO @ Sun, 21 Jun 2020 19:31:18: 11000000 INFO @ Sun, 21 Jun 2020 19:31:22: 6000000 INFO @ Sun, 21 Jun 2020 19:31:24: 12000000 INFO @ Sun, 21 Jun 2020 19:31:27: 7000000 INFO @ Sun, 21 Jun 2020 19:31:29: 13000000 INFO @ Sun, 21 Jun 2020 19:31:32: 8000000 INFO @ Sun, 21 Jun 2020 19:31:34: 14000000 INFO @ Sun, 21 Jun 2020 19:31:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:35: #1 total tags in treatment: 14142399 INFO @ Sun, 21 Jun 2020 19:31:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:31:36: #1 tags after filtering in treatment: 14142399 INFO @ Sun, 21 Jun 2020 19:31:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:37: #2 number of paired peaks: 340 WARNING @ Sun, 21 Jun 2020 19:31:37: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:37: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:31:37: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:31:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.10_model.r WARNING @ Sun, 21 Jun 2020 19:31:37: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:31:37: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:31:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:31:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:38: 9000000 INFO @ Sun, 21 Jun 2020 19:31:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:43: 10000000 INFO @ Sun, 21 Jun 2020 19:31:48: 11000000 INFO @ Sun, 21 Jun 2020 19:31:53: 12000000 INFO @ Sun, 21 Jun 2020 19:31:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.05_summits.bed INFO @ Sun, 21 Jun 2020 19:31:55: Done! pass1 - making usageList (569 chroms): 1 millis pass2 - checking and writing primary data (2354 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:31:58: 13000000 INFO @ Sun, 21 Jun 2020 19:32:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:03: 14000000 INFO @ Sun, 21 Jun 2020 19:32:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:04: #1 total tags in treatment: 14142399 INFO @ Sun, 21 Jun 2020 19:32:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:32:05: #1 tags after filtering in treatment: 14142399 INFO @ Sun, 21 Jun 2020 19:32:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:05: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:06: #2 number of paired peaks: 340 WARNING @ Sun, 21 Jun 2020 19:32:06: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Sun, 21 Jun 2020 19:32:06: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:06: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:06: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:06: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:06: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:32:06: #2 alternative fragment length(s) may be 3,39 bps INFO @ Sun, 21 Jun 2020 19:32:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.20_model.r WARNING @ Sun, 21 Jun 2020 19:32:06: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:32:06: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Sun, 21 Jun 2020 19:32:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:32:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:06: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:32:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.10_summits.bed INFO @ Sun, 21 Jun 2020 19:32:16: Done! pass1 - making usageList (441 chroms): 1 millis pass2 - checking and writing primary data (1306 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:32:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:32:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288012/SRX288012.20_summits.bed INFO @ Sun, 21 Jun 2020 19:32:46: Done! pass1 - making usageList (221 chroms): 0 millis pass2 - checking and writing primary data (449 records, 4 fields): 9 millis CompletedMACS2peakCalling