Job ID = 6527939 SRX = SRX331378 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:44:26 prefetch.2.10.7: 1) Downloading 'SRR947615'... 2020-06-29T13:44:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:48:47 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:48:47 prefetch.2.10.7: 1) 'SRR947615' was downloaded successfully Read 21559305 spots for SRR947615/SRR947615.sra Written 21559305 spots for SRR947615/SRR947615.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: 00:06:51 21559305 reads; of these: 21559305 (100.00%) were unpaired; of these: 1335757 (6.20%) aligned 0 times 15428650 (71.56%) aligned exactly 1 time 4794898 (22.24%) aligned >1 times 93.80% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 1890304 / 20223548 = 0.0935 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 @ Mon, 29 Jun 2020 23:06:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.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 @ Mon, 29 Jun 2020 23:06:34: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:06:34: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:06:40: 1000000 INFO @ Mon, 29 Jun 2020 23:06:46: 2000000 INFO @ Mon, 29 Jun 2020 23:06:52: 3000000 INFO @ Mon, 29 Jun 2020 23:06:57: 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 @ Mon, 29 Jun 2020 23:07:03: 5000000 INFO @ Mon, 29 Jun 2020 23:07:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.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 @ Mon, 29 Jun 2020 23:07:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:07:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:07:10: 6000000 INFO @ Mon, 29 Jun 2020 23:07:10: 1000000 INFO @ Mon, 29 Jun 2020 23:07:17: 7000000 INFO @ Mon, 29 Jun 2020 23:07:17: 2000000 INFO @ Mon, 29 Jun 2020 23:07:23: 8000000 INFO @ Mon, 29 Jun 2020 23:07:24: 3000000 INFO @ Mon, 29 Jun 2020 23:07:30: 9000000 INFO @ Mon, 29 Jun 2020 23:07:31: 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 @ Mon, 29 Jun 2020 23:07:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.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 @ Mon, 29 Jun 2020 23:07:34: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:07:34: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:07:37: 10000000 INFO @ Mon, 29 Jun 2020 23:07:37: 5000000 INFO @ Mon, 29 Jun 2020 23:07:41: 1000000 INFO @ Mon, 29 Jun 2020 23:07:44: 11000000 INFO @ Mon, 29 Jun 2020 23:07:44: 6000000 INFO @ Mon, 29 Jun 2020 23:07:48: 2000000 INFO @ Mon, 29 Jun 2020 23:07:50: 12000000 INFO @ Mon, 29 Jun 2020 23:07:51: 7000000 INFO @ Mon, 29 Jun 2020 23:07:54: 3000000 INFO @ Mon, 29 Jun 2020 23:07:57: 13000000 INFO @ Mon, 29 Jun 2020 23:07:58: 8000000 INFO @ Mon, 29 Jun 2020 23:08:01: 4000000 INFO @ Mon, 29 Jun 2020 23:08:04: 14000000 INFO @ Mon, 29 Jun 2020 23:08:05: 9000000 INFO @ Mon, 29 Jun 2020 23:08:08: 5000000 INFO @ Mon, 29 Jun 2020 23:08:11: 15000000 INFO @ Mon, 29 Jun 2020 23:08:11: 10000000 INFO @ Mon, 29 Jun 2020 23:08:15: 6000000 INFO @ Mon, 29 Jun 2020 23:08:18: 16000000 INFO @ Mon, 29 Jun 2020 23:08:18: 11000000 INFO @ Mon, 29 Jun 2020 23:08:22: 7000000 INFO @ Mon, 29 Jun 2020 23:08:25: 17000000 INFO @ Mon, 29 Jun 2020 23:08:25: 12000000 INFO @ Mon, 29 Jun 2020 23:08:28: 8000000 INFO @ Mon, 29 Jun 2020 23:08:32: 13000000 INFO @ Mon, 29 Jun 2020 23:08:32: 18000000 INFO @ Mon, 29 Jun 2020 23:08:34: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:08:34: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:08:34: #1 total tags in treatment: 18333244 INFO @ Mon, 29 Jun 2020 23:08:34: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:08:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:08:35: #1 tags after filtering in treatment: 18333244 INFO @ Mon, 29 Jun 2020 23:08:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:08:35: #1 finished! INFO @ Mon, 29 Jun 2020 23:08:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:08:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:08:35: 9000000 INFO @ Mon, 29 Jun 2020 23:08:36: #2 number of paired peaks: 159 WARNING @ Mon, 29 Jun 2020 23:08:36: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 29 Jun 2020 23:08:36: start model_add_line... INFO @ Mon, 29 Jun 2020 23:08:36: start X-correlation... INFO @ Mon, 29 Jun 2020 23:08:36: end of X-cor INFO @ Mon, 29 Jun 2020 23:08:36: #2 finished! INFO @ Mon, 29 Jun 2020 23:08:36: #2 predicted fragment length is 40 bps INFO @ Mon, 29 Jun 2020 23:08:36: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 29 Jun 2020 23:08:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.05_model.r WARNING @ Mon, 29 Jun 2020 23:08:36: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:08:36: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 29 Jun 2020 23:08:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:08:36: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:08:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:08:38: 14000000 INFO @ Mon, 29 Jun 2020 23:08:42: 10000000 INFO @ Mon, 29 Jun 2020 23:08:45: 15000000 INFO @ Mon, 29 Jun 2020 23:08:49: 11000000 INFO @ Mon, 29 Jun 2020 23:08:52: 16000000 INFO @ Mon, 29 Jun 2020 23:08:56: 12000000 INFO @ Mon, 29 Jun 2020 23:08:59: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:09:02: 13000000 INFO @ Mon, 29 Jun 2020 23:09:06: 18000000 INFO @ Mon, 29 Jun 2020 23:09:08: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:09:08: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:09:08: #1 total tags in treatment: 18333244 INFO @ Mon, 29 Jun 2020 23:09:08: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:09:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:09:08: #1 tags after filtering in treatment: 18333244 INFO @ Mon, 29 Jun 2020 23:09:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:09:08: #1 finished! INFO @ Mon, 29 Jun 2020 23:09:08: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:09:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:09:09: 14000000 INFO @ Mon, 29 Jun 2020 23:09:10: #2 number of paired peaks: 159 WARNING @ Mon, 29 Jun 2020 23:09:10: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 29 Jun 2020 23:09:10: start model_add_line... INFO @ Mon, 29 Jun 2020 23:09:10: start X-correlation... INFO @ Mon, 29 Jun 2020 23:09:10: end of X-cor INFO @ Mon, 29 Jun 2020 23:09:10: #2 finished! INFO @ Mon, 29 Jun 2020 23:09:10: #2 predicted fragment length is 40 bps INFO @ Mon, 29 Jun 2020 23:09:10: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 29 Jun 2020 23:09:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.10_model.r WARNING @ Mon, 29 Jun 2020 23:09:10: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:09:10: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 29 Jun 2020 23:09:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:09:10: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:09:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:09:10: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:09:15: 15000000 INFO @ Mon, 29 Jun 2020 23:09:21: 16000000 INFO @ Mon, 29 Jun 2020 23:09:28: 17000000 INFO @ Mon, 29 Jun 2020 23:09:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:09:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:09:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.05_summits.bed INFO @ Mon, 29 Jun 2020 23:09:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2013 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:09:34: 18000000 INFO @ Mon, 29 Jun 2020 23:09:36: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:09:36: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:09:36: #1 total tags in treatment: 18333244 INFO @ Mon, 29 Jun 2020 23:09:36: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:09:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:09:37: #1 tags after filtering in treatment: 18333244 INFO @ Mon, 29 Jun 2020 23:09:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:09:37: #1 finished! INFO @ Mon, 29 Jun 2020 23:09:37: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:09:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:09:38: #2 number of paired peaks: 159 WARNING @ Mon, 29 Jun 2020 23:09:38: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Mon, 29 Jun 2020 23:09:38: start model_add_line... INFO @ Mon, 29 Jun 2020 23:09:38: start X-correlation... INFO @ Mon, 29 Jun 2020 23:09:38: end of X-cor INFO @ Mon, 29 Jun 2020 23:09:38: #2 finished! INFO @ Mon, 29 Jun 2020 23:09:38: #2 predicted fragment length is 40 bps INFO @ Mon, 29 Jun 2020 23:09:38: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 29 Jun 2020 23:09:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.20_model.r WARNING @ Mon, 29 Jun 2020 23:09:38: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:09:38: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 29 Jun 2020 23:09:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:09:38: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:09:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:09:43: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:09:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:09:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:09:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.10_summits.bed INFO @ Mon, 29 Jun 2020 23:09:59: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1608 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:10:12: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:10:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:10:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:10:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331378/SRX331378.20_summits.bed INFO @ Mon, 29 Jun 2020 23:10:28: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1053 records, 4 fields): 2 millis CompletedMACS2peakCalling