Job ID = 6456263 SRX = SRX331413 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:36:59 prefetch.2.10.7: 1) Downloading 'SRR947650'... 2020-06-21T10:36:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:41:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:41:48 prefetch.2.10.7: 1) 'SRR947650' was downloaded successfully Read 21575683 spots for SRR947650/SRR947650.sra Written 21575683 spots for SRR947650/SRR947650.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:49 21575683 reads; of these: 21575683 (100.00%) were unpaired; of these: 3111473 (14.42%) aligned 0 times 12219091 (56.63%) aligned exactly 1 time 6245119 (28.95%) aligned >1 times 85.58% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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] 3001631 / 18464210 = 0.1626 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 19:53:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.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 19:53:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:53:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:53:36: 1000000 INFO @ Sun, 21 Jun 2020 19:53:41: 2000000 INFO @ Sun, 21 Jun 2020 19:53:46: 3000000 INFO @ Sun, 21 Jun 2020 19:53:52: 4000000 INFO @ Sun, 21 Jun 2020 19:53:57: 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 @ Sun, 21 Jun 2020 19:54:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.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 19:54:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:03: 6000000 INFO @ Sun, 21 Jun 2020 19:54:06: 1000000 INFO @ Sun, 21 Jun 2020 19:54:08: 7000000 INFO @ Sun, 21 Jun 2020 19:54:12: 2000000 INFO @ Sun, 21 Jun 2020 19:54:14: 8000000 INFO @ Sun, 21 Jun 2020 19:54:18: 3000000 INFO @ Sun, 21 Jun 2020 19:54:20: 9000000 INFO @ Sun, 21 Jun 2020 19:54:23: 4000000 INFO @ Sun, 21 Jun 2020 19:54:25: 10000000 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 19:54:30: 5000000 INFO @ Sun, 21 Jun 2020 19:54:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.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 19:54:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:31: 11000000 INFO @ Sun, 21 Jun 2020 19:54:36: 6000000 INFO @ Sun, 21 Jun 2020 19:54:36: 1000000 INFO @ Sun, 21 Jun 2020 19:54:37: 12000000 INFO @ Sun, 21 Jun 2020 19:54:42: 7000000 INFO @ Sun, 21 Jun 2020 19:54:42: 2000000 INFO @ Sun, 21 Jun 2020 19:54:43: 13000000 INFO @ Sun, 21 Jun 2020 19:54:47: 8000000 INFO @ Sun, 21 Jun 2020 19:54:48: 14000000 INFO @ Sun, 21 Jun 2020 19:54:48: 3000000 INFO @ Sun, 21 Jun 2020 19:54:53: 9000000 INFO @ Sun, 21 Jun 2020 19:54:54: 15000000 INFO @ Sun, 21 Jun 2020 19:54:55: 4000000 INFO @ Sun, 21 Jun 2020 19:54:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:54:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:54:57: #1 total tags in treatment: 15462579 INFO @ Sun, 21 Jun 2020 19:54:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:57: #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 19:54:57: #1 tags after filtering in treatment: 15462508 INFO @ Sun, 21 Jun 2020 19:54:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:57: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:58: #2 number of paired peaks: 1437 INFO @ Sun, 21 Jun 2020 19:54:58: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:59: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:54:59: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 19:54:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.05_model.r WARNING @ Sun, 21 Jun 2020 19:54:59: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:54:59: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 19:54:59: #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 19:54:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:59: 10000000 INFO @ Sun, 21 Jun 2020 19:55:01: 5000000 INFO @ Sun, 21 Jun 2020 19:55:04: 11000000 INFO @ Sun, 21 Jun 2020 19:55:08: 6000000 INFO @ Sun, 21 Jun 2020 19:55:10: 12000000 INFO @ Sun, 21 Jun 2020 19:55:14: 7000000 INFO @ Sun, 21 Jun 2020 19:55:16: 13000000 INFO @ Sun, 21 Jun 2020 19:55:20: 8000000 INFO @ Sun, 21 Jun 2020 19:55:21: 14000000 INFO @ Sun, 21 Jun 2020 19:55:27: 15000000 INFO @ Sun, 21 Jun 2020 19:55:27: 9000000 INFO @ Sun, 21 Jun 2020 19:55:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:55:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:55:30: #1 total tags in treatment: 15462579 INFO @ Sun, 21 Jun 2020 19:55:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:30: #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 19:55:30: #1 tags after filtering in treatment: 15462508 INFO @ Sun, 21 Jun 2020 19:55:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:32: #2 number of paired peaks: 1437 INFO @ Sun, 21 Jun 2020 19:55:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:55:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:32: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:32: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:32: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:55:32: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 19:55:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.10_model.r WARNING @ Sun, 21 Jun 2020 19:55:32: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:55:32: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 19:55:32: #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 19:55:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:34: 10000000 INFO @ Sun, 21 Jun 2020 19:55:40: 11000000 INFO @ Sun, 21 Jun 2020 19:55:46: 12000000 INFO @ Sun, 21 Jun 2020 19:55:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.05_summits.bed INFO @ Sun, 21 Jun 2020 19:55:48: Done! pass1 - making usageList (613 chroms): 2 millis pass2 - checking and writing primary data (2428 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:55:53: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:55:59: 14000000 INFO @ Sun, 21 Jun 2020 19:56:05: 15000000 INFO @ Sun, 21 Jun 2020 19:56:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:56:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:56:09: #1 total tags in treatment: 15462579 INFO @ Sun, 21 Jun 2020 19:56:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:09: #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 19:56:09: #1 tags after filtering in treatment: 15462508 INFO @ Sun, 21 Jun 2020 19:56:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:09: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:10: #2 number of paired peaks: 1437 INFO @ Sun, 21 Jun 2020 19:56:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:11: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:56:11: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 19:56:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.20_model.r WARNING @ Sun, 21 Jun 2020 19:56:11: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:56:11: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 19:56:11: #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 19:56:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.10_summits.bed INFO @ Sun, 21 Jun 2020 19:56:23: Done! pass1 - making usageList (542 chroms): 1 millis pass2 - checking and writing primary data (2062 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:56:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:57:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331413/SRX331413.20_summits.bed INFO @ Sun, 21 Jun 2020 19:57:02: Done! pass1 - making usageList (472 chroms): 1 millis pass2 - checking and writing primary data (1545 records, 4 fields): 17 millis CompletedMACS2peakCalling