Job ID = 6456625 SRX = SRX373366 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:03:01 prefetch.2.10.7: 1) Downloading 'SRR1024325'... 2020-06-21T11:03:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:09:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:09:16 prefetch.2.10.7: 1) 'SRR1024325' was downloaded successfully Read 30298852 spots for SRR1024325/SRR1024325.sra Written 30298852 spots for SRR1024325/SRR1024325.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: 00:07:19 30298852 reads; of these: 30298852 (100.00%) were unpaired; of these: 4434224 (14.63%) aligned 0 times 20061353 (66.21%) aligned exactly 1 time 5803275 (19.15%) aligned >1 times 85.37% overall alignment rate Time searching: 00:07:19 Overall time: 00:07:19 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] 7882449 / 25864628 = 0.3048 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 20:24:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.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 20:24:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:12: 1000000 INFO @ Sun, 21 Jun 2020 20:24:17: 2000000 INFO @ Sun, 21 Jun 2020 20:24:22: 3000000 INFO @ Sun, 21 Jun 2020 20:24:27: 4000000 INFO @ Sun, 21 Jun 2020 20:24:32: 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 20:24:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.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 20:24:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:37: 6000000 INFO @ Sun, 21 Jun 2020 20:24:43: 7000000 INFO @ Sun, 21 Jun 2020 20:24:43: 1000000 INFO @ Sun, 21 Jun 2020 20:24:48: 8000000 INFO @ Sun, 21 Jun 2020 20:24:49: 2000000 INFO @ Sun, 21 Jun 2020 20:24:53: 9000000 INFO @ Sun, 21 Jun 2020 20:24:56: 3000000 INFO @ Sun, 21 Jun 2020 20:24:59: 10000000 INFO @ Sun, 21 Jun 2020 20:25:02: 4000000 INFO @ Sun, 21 Jun 2020 20:25:04: 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 @ Sun, 21 Jun 2020 20:25:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.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 20:25:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:08: 5000000 INFO @ Sun, 21 Jun 2020 20:25:09: 12000000 INFO @ Sun, 21 Jun 2020 20:25:12: 1000000 INFO @ Sun, 21 Jun 2020 20:25:14: 6000000 INFO @ Sun, 21 Jun 2020 20:25:15: 13000000 INFO @ Sun, 21 Jun 2020 20:25:18: 2000000 INFO @ Sun, 21 Jun 2020 20:25:20: 7000000 INFO @ Sun, 21 Jun 2020 20:25:21: 14000000 INFO @ Sun, 21 Jun 2020 20:25:24: 3000000 INFO @ Sun, 21 Jun 2020 20:25:26: 8000000 INFO @ Sun, 21 Jun 2020 20:25:26: 15000000 INFO @ Sun, 21 Jun 2020 20:25:29: 4000000 INFO @ Sun, 21 Jun 2020 20:25:32: 16000000 INFO @ Sun, 21 Jun 2020 20:25:32: 9000000 INFO @ Sun, 21 Jun 2020 20:25:35: 5000000 INFO @ Sun, 21 Jun 2020 20:25:37: 17000000 INFO @ Sun, 21 Jun 2020 20:25:38: 10000000 INFO @ Sun, 21 Jun 2020 20:25:40: 6000000 INFO @ Sun, 21 Jun 2020 20:25:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:25:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:25:43: #1 total tags in treatment: 17982179 INFO @ Sun, 21 Jun 2020 20:25:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:25:43: #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 20:25:44: #1 tags after filtering in treatment: 17982092 INFO @ Sun, 21 Jun 2020 20:25:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:25:44: #1 finished! INFO @ Sun, 21 Jun 2020 20:25:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:25:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:25:44: 11000000 INFO @ Sun, 21 Jun 2020 20:25:45: #2 number of paired peaks: 1059 INFO @ Sun, 21 Jun 2020 20:25:45: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:45: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:45: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:45: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:45: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 20:25:45: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sun, 21 Jun 2020 20:25:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.05_model.r WARNING @ Sun, 21 Jun 2020 20:25:45: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:25:45: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sun, 21 Jun 2020 20:25:45: #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 20:25:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:25:46: 7000000 INFO @ Sun, 21 Jun 2020 20:25:50: 12000000 INFO @ Sun, 21 Jun 2020 20:25:51: 8000000 INFO @ Sun, 21 Jun 2020 20:25:56: 13000000 INFO @ Sun, 21 Jun 2020 20:25:57: 9000000 INFO @ Sun, 21 Jun 2020 20:26:02: 10000000 INFO @ Sun, 21 Jun 2020 20:26:03: 14000000 INFO @ Sun, 21 Jun 2020 20:26:08: 11000000 INFO @ Sun, 21 Jun 2020 20:26:08: 15000000 INFO @ Sun, 21 Jun 2020 20:26:13: 12000000 INFO @ Sun, 21 Jun 2020 20:26:14: 16000000 INFO @ Sun, 21 Jun 2020 20:26:19: 13000000 INFO @ Sun, 21 Jun 2020 20:26:20: 17000000 INFO @ Sun, 21 Jun 2020 20:26:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:26:25: 14000000 INFO @ Sun, 21 Jun 2020 20:26:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:26:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:26:27: #1 total tags in treatment: 17982179 INFO @ Sun, 21 Jun 2020 20:26:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:26:27: #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 20:26:27: #1 tags after filtering in treatment: 17982092 INFO @ Sun, 21 Jun 2020 20:26:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:26:27: #1 finished! INFO @ Sun, 21 Jun 2020 20:26:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:26:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:26:28: #2 number of paired peaks: 1059 INFO @ Sun, 21 Jun 2020 20:26:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:26:29: start X-correlation... INFO @ Sun, 21 Jun 2020 20:26:29: end of X-cor INFO @ Sun, 21 Jun 2020 20:26:29: #2 finished! INFO @ Sun, 21 Jun 2020 20:26:29: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 20:26:29: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sun, 21 Jun 2020 20:26:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.10_model.r WARNING @ Sun, 21 Jun 2020 20:26:29: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:26:29: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sun, 21 Jun 2020 20:26:29: #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 20:26:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:26:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:26:30: 15000000 INFO @ Sun, 21 Jun 2020 20:26:35: 16000000 INFO @ Sun, 21 Jun 2020 20:26:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.05_summits.bed INFO @ Sun, 21 Jun 2020 20:26:39: Done! pass1 - making usageList (521 chroms): 1 millis pass2 - checking and writing primary data (3144 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:26:40: 17000000 INFO @ Sun, 21 Jun 2020 20:26:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:26:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:26:46: #1 total tags in treatment: 17982179 INFO @ Sun, 21 Jun 2020 20:26:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:26:46: #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 20:26:46: #1 tags after filtering in treatment: 17982092 INFO @ Sun, 21 Jun 2020 20:26:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:26:46: #1 finished! INFO @ Sun, 21 Jun 2020 20:26:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:26:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:26:48: #2 number of paired peaks: 1059 INFO @ Sun, 21 Jun 2020 20:26:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:26:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:26:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:26:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:26:48: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 20:26:48: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sun, 21 Jun 2020 20:26:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.20_model.r WARNING @ Sun, 21 Jun 2020 20:26:48: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:26:48: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sun, 21 Jun 2020 20:26:48: #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 20:26:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:27:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:27:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:27:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:27:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.10_summits.bed INFO @ Sun, 21 Jun 2020 20:27:18: Done! pass1 - making usageList (325 chroms): 2 millis pass2 - checking and writing primary data (1624 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:27:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:27:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:27:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:27:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX373366/SRX373366.20_summits.bed INFO @ Sun, 21 Jun 2020 20:27:40: Done! pass1 - making usageList (251 chroms): 1 millis pass2 - checking and writing primary data (840 records, 4 fields): 11 millis CompletedMACS2peakCalling