Job ID = 6453745 SRX = SRX1433391 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:57:49 prefetch.2.10.7: 1) Downloading 'SRR2919807'... 2020-06-21T08:57:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:02:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:02:47 prefetch.2.10.7: 1) 'SRR2919807' was downloaded successfully Read 26926875 spots for SRR2919807/SRR2919807.sra Written 26926875 spots for SRR2919807/SRR2919807.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: 00:06:06 26926875 reads; of these: 26926875 (100.00%) were unpaired; of these: 991159 (3.68%) aligned 0 times 19654978 (72.99%) aligned exactly 1 time 6280738 (23.33%) aligned >1 times 96.32% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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 12 files... [bam_rmdupse_core] 4049783 / 25935716 = 0.1561 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 18:15:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.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 18:15:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:17: 1000000 INFO @ Sun, 21 Jun 2020 18:15:22: 2000000 INFO @ Sun, 21 Jun 2020 18:15:26: 3000000 INFO @ Sun, 21 Jun 2020 18:15:31: 4000000 INFO @ Sun, 21 Jun 2020 18:15:35: 5000000 INFO @ Sun, 21 Jun 2020 18:15:40: 6000000 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 18:15:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.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 18:15:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:15:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:44: 7000000 INFO @ Sun, 21 Jun 2020 18:15:48: 1000000 INFO @ Sun, 21 Jun 2020 18:15:49: 8000000 INFO @ Sun, 21 Jun 2020 18:15:52: 2000000 INFO @ Sun, 21 Jun 2020 18:15:53: 9000000 INFO @ Sun, 21 Jun 2020 18:15:57: 3000000 INFO @ Sun, 21 Jun 2020 18:15:58: 10000000 INFO @ Sun, 21 Jun 2020 18:16:01: 4000000 INFO @ Sun, 21 Jun 2020 18:16:02: 11000000 INFO @ Sun, 21 Jun 2020 18:16:06: 5000000 INFO @ Sun, 21 Jun 2020 18:16:07: 12000000 INFO @ Sun, 21 Jun 2020 18:16:10: 6000000 INFO @ Sun, 21 Jun 2020 18:16:11: 13000000 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 18:16:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.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 18:16:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:15: 7000000 INFO @ Sun, 21 Jun 2020 18:16:16: 14000000 INFO @ Sun, 21 Jun 2020 18:16:18: 1000000 INFO @ Sun, 21 Jun 2020 18:16:19: 8000000 INFO @ Sun, 21 Jun 2020 18:16:20: 15000000 INFO @ Sun, 21 Jun 2020 18:16:24: 2000000 INFO @ Sun, 21 Jun 2020 18:16:24: 9000000 INFO @ Sun, 21 Jun 2020 18:16:25: 16000000 INFO @ Sun, 21 Jun 2020 18:16:29: 10000000 INFO @ Sun, 21 Jun 2020 18:16:29: 3000000 INFO @ Sun, 21 Jun 2020 18:16:29: 17000000 INFO @ Sun, 21 Jun 2020 18:16:33: 11000000 INFO @ Sun, 21 Jun 2020 18:16:34: 18000000 INFO @ Sun, 21 Jun 2020 18:16:35: 4000000 INFO @ Sun, 21 Jun 2020 18:16:38: 12000000 INFO @ Sun, 21 Jun 2020 18:16:39: 19000000 INFO @ Sun, 21 Jun 2020 18:16:40: 5000000 INFO @ Sun, 21 Jun 2020 18:16:42: 13000000 INFO @ Sun, 21 Jun 2020 18:16:43: 20000000 INFO @ Sun, 21 Jun 2020 18:16:45: 6000000 INFO @ Sun, 21 Jun 2020 18:16:47: 14000000 INFO @ Sun, 21 Jun 2020 18:16:48: 21000000 INFO @ Sun, 21 Jun 2020 18:16:50: 7000000 INFO @ Sun, 21 Jun 2020 18:16:51: 15000000 INFO @ Sun, 21 Jun 2020 18:16:52: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:16:52: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:16:52: #1 total tags in treatment: 21885933 INFO @ Sun, 21 Jun 2020 18:16:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:52: #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 18:16:53: #1 tags after filtering in treatment: 21885858 INFO @ Sun, 21 Jun 2020 18:16:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:54: #2 number of paired peaks: 504 WARNING @ Sun, 21 Jun 2020 18:16:54: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Sun, 21 Jun 2020 18:16:54: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:54: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:54: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:54: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:54: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:16:54: #2 alternative fragment length(s) may be 2,52,580 bps INFO @ Sun, 21 Jun 2020 18:16:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.05_model.r WARNING @ Sun, 21 Jun 2020 18:16:54: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:16:54: #2 You may need to consider one of the other alternative d(s): 2,52,580 WARNING @ Sun, 21 Jun 2020 18:16:54: #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 18:16:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:16:56: 16000000 INFO @ Sun, 21 Jun 2020 18:16:56: 8000000 INFO @ Sun, 21 Jun 2020 18:17:00: 17000000 INFO @ Sun, 21 Jun 2020 18:17:02: 9000000 INFO @ Sun, 21 Jun 2020 18:17:05: 18000000 INFO @ Sun, 21 Jun 2020 18:17:07: 10000000 INFO @ Sun, 21 Jun 2020 18:17:10: 19000000 INFO @ Sun, 21 Jun 2020 18:17:12: 11000000 INFO @ Sun, 21 Jun 2020 18:17:14: 20000000 INFO @ Sun, 21 Jun 2020 18:17:17: 12000000 INFO @ Sun, 21 Jun 2020 18:17:19: 21000000 INFO @ Sun, 21 Jun 2020 18:17:22: 13000000 INFO @ Sun, 21 Jun 2020 18:17:23: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:17:23: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:17:23: #1 total tags in treatment: 21885933 INFO @ Sun, 21 Jun 2020 18:17:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:23: #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 18:17:24: #1 tags after filtering in treatment: 21885858 INFO @ Sun, 21 Jun 2020 18:17:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:25: #2 number of paired peaks: 504 WARNING @ Sun, 21 Jun 2020 18:17:25: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Sun, 21 Jun 2020 18:17:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:25: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:17:25: #2 alternative fragment length(s) may be 2,52,580 bps INFO @ Sun, 21 Jun 2020 18:17:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.10_model.r WARNING @ Sun, 21 Jun 2020 18:17:25: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:17:25: #2 You may need to consider one of the other alternative d(s): 2,52,580 WARNING @ Sun, 21 Jun 2020 18:17:25: #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 18:17:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:27: 14000000 INFO @ Sun, 21 Jun 2020 18:17:32: 15000000 INFO @ Sun, 21 Jun 2020 18:17:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:37: 16000000 INFO @ Sun, 21 Jun 2020 18:17:43: 17000000 INFO @ Sun, 21 Jun 2020 18:17:48: 18000000 INFO @ Sun, 21 Jun 2020 18:17:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.05_summits.bed INFO @ Sun, 21 Jun 2020 18:17:51: Done! pass1 - making usageList (297 chroms): 1 millis pass2 - checking and writing primary data (1650 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:17:53: 19000000 INFO @ Sun, 21 Jun 2020 18:17:58: 20000000 INFO @ Sun, 21 Jun 2020 18:18:03: 21000000 INFO @ Sun, 21 Jun 2020 18:18:04: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:18:08: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:18:08: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:18:08: #1 total tags in treatment: 21885933 INFO @ Sun, 21 Jun 2020 18:18:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:08: #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 18:18:09: #1 tags after filtering in treatment: 21885858 INFO @ Sun, 21 Jun 2020 18:18:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:10: #2 number of paired peaks: 504 WARNING @ Sun, 21 Jun 2020 18:18:10: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Sun, 21 Jun 2020 18:18:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:10: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:18:10: #2 alternative fragment length(s) may be 2,52,580 bps INFO @ Sun, 21 Jun 2020 18:18:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.20_model.r WARNING @ Sun, 21 Jun 2020 18:18:10: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:18:10: #2 You may need to consider one of the other alternative d(s): 2,52,580 WARNING @ Sun, 21 Jun 2020 18:18:10: #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 18:18:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:18:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.10_summits.bed INFO @ Sun, 21 Jun 2020 18:18:23: Done! pass1 - making usageList (197 chroms): 1 millis pass2 - checking and writing primary data (800 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:18:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:19:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:19:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:19:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433391/SRX1433391.20_summits.bed INFO @ Sun, 21 Jun 2020 18:19:06: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (328 records, 4 fields): 4 millis CompletedMACS2peakCalling