Job ID = 6508747 SRX = SRX467103 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:07:29 prefetch.2.10.7: 1) Downloading 'SRR1164527'... 2020-06-26T15:07:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:09:04 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:09:04 prefetch.2.10.7: 1) 'SRR1164527' was downloaded successfully Read 16164431 spots for SRR1164527/SRR1164527.sra Written 16164431 spots for SRR1164527/SRR1164527.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: 00:04:38 16164431 reads; of these: 16164431 (100.00%) were unpaired; of these: 1194608 (7.39%) aligned 0 times 11266154 (69.70%) aligned exactly 1 time 3703669 (22.91%) aligned >1 times 92.61% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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] 1685453 / 14969823 = 0.1126 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 @ Sat, 27 Jun 2020 00:19:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.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 @ Sat, 27 Jun 2020 00:19:50: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:19:50: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:19:55: 1000000 INFO @ Sat, 27 Jun 2020 00:20:01: 2000000 INFO @ Sat, 27 Jun 2020 00:20:07: 3000000 INFO @ Sat, 27 Jun 2020 00:20:13: 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 @ Sat, 27 Jun 2020 00:20:19: 5000000 INFO @ Sat, 27 Jun 2020 00:20:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.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 @ Sat, 27 Jun 2020 00:20:20: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:20:20: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:20:25: 6000000 INFO @ Sat, 27 Jun 2020 00:20:26: 1000000 INFO @ Sat, 27 Jun 2020 00:20:31: 7000000 INFO @ Sat, 27 Jun 2020 00:20:33: 2000000 INFO @ Sat, 27 Jun 2020 00:20:38: 8000000 INFO @ Sat, 27 Jun 2020 00:20:39: 3000000 INFO @ Sat, 27 Jun 2020 00:20:44: 9000000 INFO @ Sat, 27 Jun 2020 00:20:46: 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 @ Sat, 27 Jun 2020 00:20:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.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 @ Sat, 27 Jun 2020 00:20:50: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:20:50: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:20:51: 10000000 INFO @ Sat, 27 Jun 2020 00:20:53: 5000000 INFO @ Sat, 27 Jun 2020 00:20:57: 1000000 INFO @ Sat, 27 Jun 2020 00:20:58: 11000000 INFO @ Sat, 27 Jun 2020 00:20:59: 6000000 INFO @ Sat, 27 Jun 2020 00:21:03: 2000000 INFO @ Sat, 27 Jun 2020 00:21:05: 12000000 INFO @ Sat, 27 Jun 2020 00:21:06: 7000000 INFO @ Sat, 27 Jun 2020 00:21:10: 3000000 INFO @ Sat, 27 Jun 2020 00:21:12: 13000000 INFO @ Sat, 27 Jun 2020 00:21:13: 8000000 INFO @ Sat, 27 Jun 2020 00:21:14: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:21:14: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:21:14: #1 total tags in treatment: 13284370 INFO @ Sat, 27 Jun 2020 00:21:14: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:21:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:21:15: #1 tags after filtering in treatment: 13284369 INFO @ Sat, 27 Jun 2020 00:21:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:21:15: #1 finished! INFO @ Sat, 27 Jun 2020 00:21:15: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:21:16: #2 number of paired peaks: 374 WARNING @ Sat, 27 Jun 2020 00:21:16: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sat, 27 Jun 2020 00:21:16: start model_add_line... INFO @ Sat, 27 Jun 2020 00:21:16: start X-correlation... INFO @ Sat, 27 Jun 2020 00:21:16: end of X-cor INFO @ Sat, 27 Jun 2020 00:21:16: #2 finished! INFO @ Sat, 27 Jun 2020 00:21:16: #2 predicted fragment length is 43 bps INFO @ Sat, 27 Jun 2020 00:21:16: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sat, 27 Jun 2020 00:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.05_model.r WARNING @ Sat, 27 Jun 2020 00:21:16: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:21:16: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sat, 27 Jun 2020 00:21:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:21:16: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:21:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:21:17: 4000000 INFO @ Sat, 27 Jun 2020 00:21:20: 9000000 INFO @ Sat, 27 Jun 2020 00:21:24: 5000000 INFO @ Sat, 27 Jun 2020 00:21:26: 10000000 INFO @ Sat, 27 Jun 2020 00:21:30: 6000000 INFO @ Sat, 27 Jun 2020 00:21:34: 11000000 INFO @ Sat, 27 Jun 2020 00:21:37: 7000000 INFO @ Sat, 27 Jun 2020 00:21:40: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:21:40: 12000000 INFO @ Sat, 27 Jun 2020 00:21:44: 8000000 INFO @ Sat, 27 Jun 2020 00:21:47: 13000000 INFO @ Sat, 27 Jun 2020 00:21:50: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:21:50: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:21:50: #1 total tags in treatment: 13284370 INFO @ Sat, 27 Jun 2020 00:21:50: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:21:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:21:50: 9000000 INFO @ Sat, 27 Jun 2020 00:21:50: #1 tags after filtering in treatment: 13284369 INFO @ Sat, 27 Jun 2020 00:21:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:21:50: #1 finished! INFO @ Sat, 27 Jun 2020 00:21:50: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:21:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:21:51: #2 number of paired peaks: 374 WARNING @ Sat, 27 Jun 2020 00:21:51: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sat, 27 Jun 2020 00:21:51: start model_add_line... INFO @ Sat, 27 Jun 2020 00:21:51: start X-correlation... INFO @ Sat, 27 Jun 2020 00:21:51: end of X-cor INFO @ Sat, 27 Jun 2020 00:21:51: #2 finished! INFO @ Sat, 27 Jun 2020 00:21:51: #2 predicted fragment length is 43 bps INFO @ Sat, 27 Jun 2020 00:21:51: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sat, 27 Jun 2020 00:21:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.10_model.r WARNING @ Sat, 27 Jun 2020 00:21:51: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:21:51: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sat, 27 Jun 2020 00:21:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:21:51: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:21:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:21:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:21:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:21:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.05_summits.bed INFO @ Sat, 27 Jun 2020 00:21:52: Done! pass1 - making usageList (516 chroms): 2 millis pass2 - checking and writing primary data (2103 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:21:57: 10000000 INFO @ Sat, 27 Jun 2020 00:22:04: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:22:11: 12000000 INFO @ Sat, 27 Jun 2020 00:22:15: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:22:18: 13000000 INFO @ Sat, 27 Jun 2020 00:22:20: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:22:20: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:22:20: #1 total tags in treatment: 13284370 INFO @ Sat, 27 Jun 2020 00:22:20: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:22:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:22:21: #1 tags after filtering in treatment: 13284369 INFO @ Sat, 27 Jun 2020 00:22:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:22:21: #1 finished! INFO @ Sat, 27 Jun 2020 00:22:21: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:22:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:22:22: #2 number of paired peaks: 374 WARNING @ Sat, 27 Jun 2020 00:22:22: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sat, 27 Jun 2020 00:22:22: start model_add_line... INFO @ Sat, 27 Jun 2020 00:22:22: start X-correlation... INFO @ Sat, 27 Jun 2020 00:22:22: end of X-cor INFO @ Sat, 27 Jun 2020 00:22:22: #2 finished! INFO @ Sat, 27 Jun 2020 00:22:22: #2 predicted fragment length is 43 bps INFO @ Sat, 27 Jun 2020 00:22:22: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sat, 27 Jun 2020 00:22:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.20_model.r WARNING @ Sat, 27 Jun 2020 00:22:22: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:22:22: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sat, 27 Jun 2020 00:22:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:22:22: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:22:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:22:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:22:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:22:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.10_summits.bed INFO @ Sat, 27 Jun 2020 00:22:28: Done! pass1 - making usageList (445 chroms): 2 millis pass2 - checking and writing primary data (1546 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:22:46: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:22:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:22:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:22:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467103/SRX467103.20_summits.bed INFO @ Sat, 27 Jun 2020 00:22:58: Done! pass1 - making usageList (243 chroms): 1 millis pass2 - checking and writing primary data (506 records, 4 fields): 15 millis CompletedMACS2peakCalling