Job ID = 6454229 SRX = SRX193308 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:09:57 prefetch.2.10.7: 1) Downloading 'SRR585041'... 2020-06-21T09:09:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:14:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:14:52 prefetch.2.10.7: 1) 'SRR585041' was downloaded successfully Read 18046993 spots for SRR585041/SRR585041.sra Written 18046993 spots for SRR585041/SRR585041.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: 00:05:02 18046993 reads; of these: 18046993 (100.00%) were unpaired; of these: 826954 (4.58%) aligned 0 times 11827760 (65.54%) aligned exactly 1 time 5392279 (29.88%) aligned >1 times 95.42% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 3085870 / 17220039 = 0.1792 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 18:25:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.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 18:25:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:35: 1000000 INFO @ Sun, 21 Jun 2020 18:25:41: 2000000 INFO @ Sun, 21 Jun 2020 18:25:46: 3000000 INFO @ Sun, 21 Jun 2020 18:25:52: 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 @ Sun, 21 Jun 2020 18:25:58: 5000000 INFO @ Sun, 21 Jun 2020 18:25:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.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 18:25:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:26:05: 6000000 INFO @ Sun, 21 Jun 2020 18:26:07: 1000000 INFO @ Sun, 21 Jun 2020 18:26:12: 7000000 INFO @ Sun, 21 Jun 2020 18:26:14: 2000000 INFO @ Sun, 21 Jun 2020 18:26:19: 8000000 INFO @ Sun, 21 Jun 2020 18:26:22: 3000000 INFO @ Sun, 21 Jun 2020 18:26:26: 9000000 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 18:26:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.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 18:26:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:26:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:26:29: 4000000 INFO @ Sun, 21 Jun 2020 18:26:33: 10000000 INFO @ Sun, 21 Jun 2020 18:26:37: 1000000 INFO @ Sun, 21 Jun 2020 18:26:37: 5000000 INFO @ Sun, 21 Jun 2020 18:26:41: 11000000 INFO @ Sun, 21 Jun 2020 18:26:44: 2000000 INFO @ Sun, 21 Jun 2020 18:26:45: 6000000 INFO @ Sun, 21 Jun 2020 18:26:48: 12000000 INFO @ Sun, 21 Jun 2020 18:26:51: 3000000 INFO @ Sun, 21 Jun 2020 18:26:52: 7000000 INFO @ Sun, 21 Jun 2020 18:26:56: 13000000 INFO @ Sun, 21 Jun 2020 18:26:59: 4000000 INFO @ Sun, 21 Jun 2020 18:27:00: 8000000 INFO @ Sun, 21 Jun 2020 18:27:03: 14000000 INFO @ Sun, 21 Jun 2020 18:27:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:27:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:27:04: #1 total tags in treatment: 14134169 INFO @ Sun, 21 Jun 2020 18:27:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:04: #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 18:27:05: #1 tags after filtering in treatment: 14134103 INFO @ Sun, 21 Jun 2020 18:27:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:06: #2 number of paired peaks: 1484 INFO @ Sun, 21 Jun 2020 18:27:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:06: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:27:06: #2 alternative fragment length(s) may be 2,50,582 bps INFO @ Sun, 21 Jun 2020 18:27:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.05_model.r WARNING @ Sun, 21 Jun 2020 18:27:06: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:27:06: #2 You may need to consider one of the other alternative d(s): 2,50,582 WARNING @ Sun, 21 Jun 2020 18:27:06: #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 18:27:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:06: 5000000 INFO @ Sun, 21 Jun 2020 18:27:08: 9000000 INFO @ Sun, 21 Jun 2020 18:27:13: 6000000 INFO @ Sun, 21 Jun 2020 18:27:15: 10000000 INFO @ Sun, 21 Jun 2020 18:27:20: 7000000 INFO @ Sun, 21 Jun 2020 18:27:23: 11000000 INFO @ Sun, 21 Jun 2020 18:27:27: 8000000 INFO @ Sun, 21 Jun 2020 18:27:31: 12000000 INFO @ Sun, 21 Jun 2020 18:27:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:27:34: 9000000 INFO @ Sun, 21 Jun 2020 18:27:38: 13000000 INFO @ Sun, 21 Jun 2020 18:27:41: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:27:46: 14000000 INFO @ Sun, 21 Jun 2020 18:27:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:27:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:27:47: #1 total tags in treatment: 14134169 INFO @ Sun, 21 Jun 2020 18:27:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:47: #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 18:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:27:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.05_summits.bed INFO @ Sun, 21 Jun 2020 18:27:48: #1 tags after filtering in treatment: 14134103 INFO @ Sun, 21 Jun 2020 18:27:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:48: Done! pass1 - making usageList (598 chroms): 1 millis pass2 - checking and writing primary data (2724 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:27:48: 11000000 INFO @ Sun, 21 Jun 2020 18:27:49: #2 number of paired peaks: 1484 INFO @ Sun, 21 Jun 2020 18:27:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:49: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:27:49: #2 alternative fragment length(s) may be 2,50,582 bps INFO @ Sun, 21 Jun 2020 18:27:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.10_model.r WARNING @ Sun, 21 Jun 2020 18:27:49: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:27:49: #2 You may need to consider one of the other alternative d(s): 2,50,582 WARNING @ Sun, 21 Jun 2020 18:27:49: #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 18:27:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:54: 12000000 INFO @ Sun, 21 Jun 2020 18:28:00: 13000000 INFO @ Sun, 21 Jun 2020 18:28:06: 14000000 INFO @ Sun, 21 Jun 2020 18:28:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:28:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:28:07: #1 total tags in treatment: 14134169 INFO @ Sun, 21 Jun 2020 18:28:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:07: #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 18:28:08: #1 tags after filtering in treatment: 14134103 INFO @ Sun, 21 Jun 2020 18:28:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:28:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:28:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:28:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:28:09: #2 number of paired peaks: 1484 INFO @ Sun, 21 Jun 2020 18:28:09: start model_add_line... INFO @ Sun, 21 Jun 2020 18:28:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:28:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:28:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:28:09: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:28:09: #2 alternative fragment length(s) may be 2,50,582 bps INFO @ Sun, 21 Jun 2020 18:28:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.20_model.r WARNING @ Sun, 21 Jun 2020 18:28:09: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:28:09: #2 You may need to consider one of the other alternative d(s): 2,50,582 WARNING @ Sun, 21 Jun 2020 18:28:09: #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 18:28:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:28:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:28:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.10_summits.bed INFO @ Sun, 21 Jun 2020 18:28:31: Done! pass1 - making usageList (525 chroms): 2 millis pass2 - checking and writing primary data (2070 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:28:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193308/SRX193308.20_summits.bed INFO @ Sun, 21 Jun 2020 18:28:50: Done! pass1 - making usageList (391 chroms): 1 millis pass2 - checking and writing primary data (994 records, 4 fields): 26 millis CompletedMACS2peakCalling