Job ID = 6454418 SRX = SRX2055950 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:19:39 prefetch.2.10.7: 1) Downloading 'SRR4069182'... 2020-06-21T09:19:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:24:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:24:52 prefetch.2.10.7: 1) 'SRR4069182' was downloaded successfully Read 23443408 spots for SRR4069182/SRR4069182.sra Written 23443408 spots for SRR4069182/SRR4069182.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: 00:06:38 23443408 reads; of these: 23443408 (100.00%) were unpaired; of these: 1941682 (8.28%) aligned 0 times 14702328 (62.71%) aligned exactly 1 time 6799398 (29.00%) aligned >1 times 91.72% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 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] 2617780 / 21501726 = 0.1217 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 18:37:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.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 18:37:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:34: 1000000 INFO @ Sun, 21 Jun 2020 18:37:39: 2000000 INFO @ Sun, 21 Jun 2020 18:37:45: 3000000 INFO @ Sun, 21 Jun 2020 18:37:51: 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 18:37:56: 5000000 INFO @ Sun, 21 Jun 2020 18:37:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.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 18:37:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:02: 6000000 INFO @ Sun, 21 Jun 2020 18:38:03: 1000000 INFO @ Sun, 21 Jun 2020 18:38:08: 7000000 INFO @ Sun, 21 Jun 2020 18:38:09: 2000000 INFO @ Sun, 21 Jun 2020 18:38:14: 8000000 INFO @ Sun, 21 Jun 2020 18:38:15: 3000000 INFO @ Sun, 21 Jun 2020 18:38:20: 9000000 INFO @ Sun, 21 Jun 2020 18:38:21: 4000000 INFO @ Sun, 21 Jun 2020 18:38:25: 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 18:38:27: 5000000 INFO @ Sun, 21 Jun 2020 18:38:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.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 18:38:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:31: 11000000 INFO @ Sun, 21 Jun 2020 18:38:33: 6000000 INFO @ Sun, 21 Jun 2020 18:38:33: 1000000 INFO @ Sun, 21 Jun 2020 18:38:37: 12000000 INFO @ Sun, 21 Jun 2020 18:38:39: 7000000 INFO @ Sun, 21 Jun 2020 18:38:39: 2000000 INFO @ Sun, 21 Jun 2020 18:38:43: 13000000 INFO @ Sun, 21 Jun 2020 18:38:45: 8000000 INFO @ Sun, 21 Jun 2020 18:38:45: 3000000 INFO @ Sun, 21 Jun 2020 18:38:49: 14000000 INFO @ Sun, 21 Jun 2020 18:38:51: 9000000 INFO @ Sun, 21 Jun 2020 18:38:51: 4000000 INFO @ Sun, 21 Jun 2020 18:38:55: 15000000 INFO @ Sun, 21 Jun 2020 18:38:57: 10000000 INFO @ Sun, 21 Jun 2020 18:38:57: 5000000 INFO @ Sun, 21 Jun 2020 18:39:01: 16000000 INFO @ Sun, 21 Jun 2020 18:39:03: 11000000 INFO @ Sun, 21 Jun 2020 18:39:03: 6000000 INFO @ Sun, 21 Jun 2020 18:39:06: 17000000 INFO @ Sun, 21 Jun 2020 18:39:09: 12000000 INFO @ Sun, 21 Jun 2020 18:39:09: 7000000 INFO @ Sun, 21 Jun 2020 18:39:12: 18000000 INFO @ Sun, 21 Jun 2020 18:39:15: 13000000 INFO @ Sun, 21 Jun 2020 18:39:15: 8000000 INFO @ Sun, 21 Jun 2020 18:39:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:39:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:39:18: #1 total tags in treatment: 18883946 INFO @ Sun, 21 Jun 2020 18:39:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:18: #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 18:39:18: #1 tags after filtering in treatment: 18883882 INFO @ Sun, 21 Jun 2020 18:39:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:20: #2 number of paired peaks: 1549 INFO @ Sun, 21 Jun 2020 18:39:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:20: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:39:20: #2 alternative fragment length(s) may be 2,50,579 bps INFO @ Sun, 21 Jun 2020 18:39:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.05_model.r WARNING @ Sun, 21 Jun 2020 18:39:20: #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 18:39:20: #2 You may need to consider one of the other alternative d(s): 2,50,579 WARNING @ Sun, 21 Jun 2020 18:39:20: #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 18:39:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:21: 14000000 INFO @ Sun, 21 Jun 2020 18:39:21: 9000000 INFO @ Sun, 21 Jun 2020 18:39:27: 15000000 INFO @ Sun, 21 Jun 2020 18:39:27: 10000000 INFO @ Sun, 21 Jun 2020 18:39:33: 16000000 INFO @ Sun, 21 Jun 2020 18:39:33: 11000000 INFO @ Sun, 21 Jun 2020 18:39:39: 17000000 INFO @ Sun, 21 Jun 2020 18:39:39: 12000000 INFO @ Sun, 21 Jun 2020 18:39:45: 18000000 INFO @ Sun, 21 Jun 2020 18:39:45: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:39:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:39:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:39:50: #1 total tags in treatment: 18883946 INFO @ Sun, 21 Jun 2020 18:39:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:50: #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 18:39:51: 14000000 INFO @ Sun, 21 Jun 2020 18:39:51: #1 tags after filtering in treatment: 18883882 INFO @ Sun, 21 Jun 2020 18:39:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:51: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:52: #2 number of paired peaks: 1549 INFO @ Sun, 21 Jun 2020 18:39:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:52: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:39:52: #2 alternative fragment length(s) may be 2,50,579 bps INFO @ Sun, 21 Jun 2020 18:39:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.10_model.r WARNING @ Sun, 21 Jun 2020 18:39:52: #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 18:39:52: #2 You may need to consider one of the other alternative d(s): 2,50,579 WARNING @ Sun, 21 Jun 2020 18:39:52: #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 18:39:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:56: 15000000 INFO @ Sun, 21 Jun 2020 18:40:02: 16000000 INFO @ Sun, 21 Jun 2020 18:40:07: 17000000 INFO @ Sun, 21 Jun 2020 18:40:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.05_summits.bed INFO @ Sun, 21 Jun 2020 18:40:12: Done! INFO @ Sun, 21 Jun 2020 18:40:12: 18000000 pass1 - making usageList (665 chroms): 2 millis pass2 - checking and writing primary data (3318 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:40:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:40:17: #1 total tags in treatment: 18883946 INFO @ Sun, 21 Jun 2020 18:40:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:17: #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 18:40:18: #1 tags after filtering in treatment: 18883882 INFO @ Sun, 21 Jun 2020 18:40:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:19: #2 number of paired peaks: 1549 INFO @ Sun, 21 Jun 2020 18:40:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:19: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:40:19: #2 alternative fragment length(s) may be 2,50,579 bps INFO @ Sun, 21 Jun 2020 18:40:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.20_model.r WARNING @ Sun, 21 Jun 2020 18:40:19: #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 18:40:19: #2 You may need to consider one of the other alternative d(s): 2,50,579 WARNING @ Sun, 21 Jun 2020 18:40:19: #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 18:40:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:40:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.10_summits.bed INFO @ Sun, 21 Jun 2020 18:40:45: Done! pass1 - making usageList (558 chroms): 2 millis pass2 - checking and writing primary data (2317 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055950/SRX2055950.20_summits.bed INFO @ Sun, 21 Jun 2020 18:41:12: Done! pass1 - making usageList (411 chroms): 1 millis pass2 - checking and writing primary data (1176 records, 4 fields): 11 millis CompletedMACS2peakCalling