Job ID = 6527779 SRX = SRX287580 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T15:01:13 prefetch.2.10.7: 1) Downloading 'SRR869723'... 2020-06-29T15:01:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:05:32 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:05:32 prefetch.2.10.7: 1) 'SRR869723' was downloaded successfully Read 32459694 spots for SRR869723/SRR869723.sra Written 32459694 spots for SRR869723/SRR869723.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:19 32459694 reads; of these: 32459694 (100.00%) were unpaired; of these: 2263442 (6.97%) aligned 0 times 21463403 (66.12%) aligned exactly 1 time 8732849 (26.90%) aligned >1 times 93.03% overall alignment rate Time searching: 00:12:20 Overall time: 00:12:20 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 16 files... [bam_rmdupse_core] 5004975 / 30196252 = 0.1657 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 @ Tue, 30 Jun 2020 00:38:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.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 @ Tue, 30 Jun 2020 00:38:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:38:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:38:18: 1000000 INFO @ Tue, 30 Jun 2020 00:38:23: 2000000 INFO @ Tue, 30 Jun 2020 00:38:29: 3000000 INFO @ Tue, 30 Jun 2020 00:38:34: 4000000 INFO @ Tue, 30 Jun 2020 00:38:39: 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 @ Tue, 30 Jun 2020 00:38:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.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 @ Tue, 30 Jun 2020 00:38:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:38:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:38:44: 6000000 INFO @ Tue, 30 Jun 2020 00:38:49: 1000000 INFO @ Tue, 30 Jun 2020 00:38:49: 7000000 INFO @ Tue, 30 Jun 2020 00:38:54: 8000000 INFO @ Tue, 30 Jun 2020 00:38:54: 2000000 INFO @ Tue, 30 Jun 2020 00:38:59: 9000000 INFO @ Tue, 30 Jun 2020 00:39:00: 3000000 INFO @ Tue, 30 Jun 2020 00:39:04: 10000000 INFO @ Tue, 30 Jun 2020 00:39:05: 4000000 INFO @ Tue, 30 Jun 2020 00:39:09: 11000000 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 @ Tue, 30 Jun 2020 00:39:11: 5000000 INFO @ Tue, 30 Jun 2020 00:39:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.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 @ Tue, 30 Jun 2020 00:39:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:39:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:39:14: 12000000 INFO @ Tue, 30 Jun 2020 00:39:17: 6000000 INFO @ Tue, 30 Jun 2020 00:39:19: 1000000 INFO @ Tue, 30 Jun 2020 00:39:20: 13000000 INFO @ Tue, 30 Jun 2020 00:39:23: 7000000 INFO @ Tue, 30 Jun 2020 00:39:25: 14000000 INFO @ Tue, 30 Jun 2020 00:39:26: 2000000 INFO @ Tue, 30 Jun 2020 00:39:29: 8000000 INFO @ Tue, 30 Jun 2020 00:39:30: 15000000 INFO @ Tue, 30 Jun 2020 00:39:32: 3000000 INFO @ Tue, 30 Jun 2020 00:39:35: 16000000 INFO @ Tue, 30 Jun 2020 00:39:35: 9000000 INFO @ Tue, 30 Jun 2020 00:39:38: 4000000 INFO @ Tue, 30 Jun 2020 00:39:40: 17000000 INFO @ Tue, 30 Jun 2020 00:39:42: 10000000 INFO @ Tue, 30 Jun 2020 00:39:44: 5000000 INFO @ Tue, 30 Jun 2020 00:39:45: 18000000 INFO @ Tue, 30 Jun 2020 00:39:48: 11000000 INFO @ Tue, 30 Jun 2020 00:39:50: 19000000 INFO @ Tue, 30 Jun 2020 00:39:51: 6000000 INFO @ Tue, 30 Jun 2020 00:39:54: 12000000 INFO @ Tue, 30 Jun 2020 00:39:56: 20000000 INFO @ Tue, 30 Jun 2020 00:39:57: 7000000 INFO @ Tue, 30 Jun 2020 00:40:00: 13000000 INFO @ Tue, 30 Jun 2020 00:40:01: 21000000 INFO @ Tue, 30 Jun 2020 00:40:03: 8000000 INFO @ Tue, 30 Jun 2020 00:40:06: 22000000 INFO @ Tue, 30 Jun 2020 00:40:06: 14000000 INFO @ Tue, 30 Jun 2020 00:40:10: 9000000 INFO @ Tue, 30 Jun 2020 00:40:11: 23000000 INFO @ Tue, 30 Jun 2020 00:40:12: 15000000 INFO @ Tue, 30 Jun 2020 00:40:16: 24000000 INFO @ Tue, 30 Jun 2020 00:40:16: 10000000 INFO @ Tue, 30 Jun 2020 00:40:19: 16000000 INFO @ Tue, 30 Jun 2020 00:40:21: 25000000 INFO @ Tue, 30 Jun 2020 00:40:22: 11000000 INFO @ Tue, 30 Jun 2020 00:40:22: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:40:22: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:40:22: #1 total tags in treatment: 25191277 INFO @ Tue, 30 Jun 2020 00:40:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:40:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:40:23: #1 tags after filtering in treatment: 25191277 INFO @ Tue, 30 Jun 2020 00:40:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:40:23: #1 finished! INFO @ Tue, 30 Jun 2020 00:40:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:40:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:40:24: #2 number of paired peaks: 131 WARNING @ Tue, 30 Jun 2020 00:40:24: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 30 Jun 2020 00:40:24: start model_add_line... INFO @ Tue, 30 Jun 2020 00:40:24: start X-correlation... INFO @ Tue, 30 Jun 2020 00:40:24: end of X-cor INFO @ Tue, 30 Jun 2020 00:40:24: #2 finished! INFO @ Tue, 30 Jun 2020 00:40:24: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 00:40:24: #2 alternative fragment length(s) may be 4,54,561,564 bps INFO @ Tue, 30 Jun 2020 00:40:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.05_model.r WARNING @ Tue, 30 Jun 2020 00:40:25: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:40:25: #2 You may need to consider one of the other alternative d(s): 4,54,561,564 WARNING @ Tue, 30 Jun 2020 00:40:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:40:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:40:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:40:25: 17000000 INFO @ Tue, 30 Jun 2020 00:40:28: 12000000 INFO @ Tue, 30 Jun 2020 00:40:31: 18000000 INFO @ Tue, 30 Jun 2020 00:40:34: 13000000 INFO @ Tue, 30 Jun 2020 00:40:37: 19000000 INFO @ Tue, 30 Jun 2020 00:40:41: 14000000 INFO @ Tue, 30 Jun 2020 00:40:43: 20000000 INFO @ Tue, 30 Jun 2020 00:40:47: 15000000 INFO @ Tue, 30 Jun 2020 00:40:49: 21000000 INFO @ Tue, 30 Jun 2020 00:40:53: 16000000 INFO @ Tue, 30 Jun 2020 00:40:56: 22000000 INFO @ Tue, 30 Jun 2020 00:40:59: 17000000 INFO @ Tue, 30 Jun 2020 00:41:02: 23000000 INFO @ Tue, 30 Jun 2020 00:41:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:41:05: 18000000 INFO @ Tue, 30 Jun 2020 00:41:08: 24000000 INFO @ Tue, 30 Jun 2020 00:41:12: 19000000 INFO @ Tue, 30 Jun 2020 00:41:14: 25000000 INFO @ Tue, 30 Jun 2020 00:41:15: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:41:15: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:41:15: #1 total tags in treatment: 25191277 INFO @ Tue, 30 Jun 2020 00:41:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:41:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:41:16: #1 tags after filtering in treatment: 25191277 INFO @ Tue, 30 Jun 2020 00:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:41:16: #1 finished! INFO @ Tue, 30 Jun 2020 00:41:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:41:17: 20000000 INFO @ Tue, 30 Jun 2020 00:41:17: #2 number of paired peaks: 131 WARNING @ Tue, 30 Jun 2020 00:41:17: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 30 Jun 2020 00:41:17: start model_add_line... INFO @ Tue, 30 Jun 2020 00:41:18: start X-correlation... INFO @ Tue, 30 Jun 2020 00:41:18: end of X-cor INFO @ Tue, 30 Jun 2020 00:41:18: #2 finished! INFO @ Tue, 30 Jun 2020 00:41:18: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 00:41:18: #2 alternative fragment length(s) may be 4,54,561,564 bps INFO @ Tue, 30 Jun 2020 00:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.10_model.r WARNING @ Tue, 30 Jun 2020 00:41:18: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:41:18: #2 You may need to consider one of the other alternative d(s): 4,54,561,564 WARNING @ Tue, 30 Jun 2020 00:41:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:41:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:41:23: 21000000 INFO @ Tue, 30 Jun 2020 00:41:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:41:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:41:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.05_summits.bed INFO @ Tue, 30 Jun 2020 00:41:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2343 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:41:29: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:41:34: 23000000 INFO @ Tue, 30 Jun 2020 00:41:39: 24000000 INFO @ Tue, 30 Jun 2020 00:41:45: 25000000 INFO @ Tue, 30 Jun 2020 00:41:46: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:41:46: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:41:46: #1 total tags in treatment: 25191277 INFO @ Tue, 30 Jun 2020 00:41:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:41:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:41:47: #1 tags after filtering in treatment: 25191277 INFO @ Tue, 30 Jun 2020 00:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:41:47: #1 finished! INFO @ Tue, 30 Jun 2020 00:41:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:41:48: #2 number of paired peaks: 131 WARNING @ Tue, 30 Jun 2020 00:41:48: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 30 Jun 2020 00:41:48: start model_add_line... INFO @ Tue, 30 Jun 2020 00:41:48: start X-correlation... INFO @ Tue, 30 Jun 2020 00:41:48: end of X-cor INFO @ Tue, 30 Jun 2020 00:41:48: #2 finished! INFO @ Tue, 30 Jun 2020 00:41:48: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 00:41:48: #2 alternative fragment length(s) may be 4,54,561,564 bps INFO @ Tue, 30 Jun 2020 00:41:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.20_model.r WARNING @ Tue, 30 Jun 2020 00:41:48: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:41:48: #2 You may need to consider one of the other alternative d(s): 4,54,561,564 WARNING @ Tue, 30 Jun 2020 00:41:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:41:48: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:41:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:41:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:42:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:42:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:42:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.10_summits.bed INFO @ Tue, 30 Jun 2020 00:42:20: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1769 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:42:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:42:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:42:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:42:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287580/SRX287580.20_summits.bed INFO @ Tue, 30 Jun 2020 00:42:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1358 records, 4 fields): 4 millis CompletedMACS2peakCalling