Job ID = 6453094 SRX = SRX1032404 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:00:12 prefetch.2.10.7: 1) Downloading 'SRR2031905'... 2020-06-21T08:00:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:09:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:09:54 prefetch.2.10.7: 1) 'SRR2031905' was downloaded successfully Read 50712068 spots for SRR2031905/SRR2031905.sra Written 50712068 spots for SRR2031905/SRR2031905.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: 00:13:51 50712068 reads; of these: 50712068 (100.00%) were unpaired; of these: 2587738 (5.10%) aligned 0 times 35015762 (69.05%) aligned exactly 1 time 13108568 (25.85%) aligned >1 times 94.90% overall alignment rate Time searching: 00:13:51 Overall time: 00:13:51 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 20 files... [bam_rmdupse_core] 22137863 / 48124330 = 0.4600 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 17:39:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.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 17:39:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:39:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:39:20: 1000000 INFO @ Sun, 21 Jun 2020 17:39:26: 2000000 INFO @ Sun, 21 Jun 2020 17:39:31: 3000000 INFO @ Sun, 21 Jun 2020 17:39:37: 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 17:39:42: 5000000 INFO @ Sun, 21 Jun 2020 17:39:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.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 17:39:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:39:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:39:48: 6000000 INFO @ Sun, 21 Jun 2020 17:39:51: 1000000 INFO @ Sun, 21 Jun 2020 17:39:54: 7000000 INFO @ Sun, 21 Jun 2020 17:39:57: 2000000 INFO @ Sun, 21 Jun 2020 17:40:01: 8000000 INFO @ Sun, 21 Jun 2020 17:40:03: 3000000 INFO @ Sun, 21 Jun 2020 17:40:07: 9000000 INFO @ Sun, 21 Jun 2020 17:40:10: 4000000 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 17:40:13: 10000000 INFO @ Sun, 21 Jun 2020 17:40:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.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 17:40:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:40:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:40:16: 5000000 INFO @ Sun, 21 Jun 2020 17:40:20: 11000000 INFO @ Sun, 21 Jun 2020 17:40:20: 1000000 INFO @ Sun, 21 Jun 2020 17:40:23: 6000000 INFO @ Sun, 21 Jun 2020 17:40:25: 2000000 INFO @ Sun, 21 Jun 2020 17:40:26: 12000000 INFO @ Sun, 21 Jun 2020 17:40:29: 7000000 INFO @ Sun, 21 Jun 2020 17:40:31: 3000000 INFO @ Sun, 21 Jun 2020 17:40:33: 13000000 INFO @ Sun, 21 Jun 2020 17:40:36: 8000000 INFO @ Sun, 21 Jun 2020 17:40:36: 4000000 INFO @ Sun, 21 Jun 2020 17:40:40: 14000000 INFO @ Sun, 21 Jun 2020 17:40:42: 5000000 INFO @ Sun, 21 Jun 2020 17:40:43: 9000000 INFO @ Sun, 21 Jun 2020 17:40:46: 15000000 INFO @ Sun, 21 Jun 2020 17:40:47: 6000000 INFO @ Sun, 21 Jun 2020 17:40:50: 10000000 INFO @ Sun, 21 Jun 2020 17:40:52: 7000000 INFO @ Sun, 21 Jun 2020 17:40:53: 16000000 INFO @ Sun, 21 Jun 2020 17:40:56: 11000000 INFO @ Sun, 21 Jun 2020 17:40:58: 8000000 INFO @ Sun, 21 Jun 2020 17:41:00: 17000000 INFO @ Sun, 21 Jun 2020 17:41:03: 12000000 INFO @ Sun, 21 Jun 2020 17:41:04: 9000000 INFO @ Sun, 21 Jun 2020 17:41:06: 18000000 INFO @ Sun, 21 Jun 2020 17:41:10: 13000000 INFO @ Sun, 21 Jun 2020 17:41:10: 10000000 INFO @ Sun, 21 Jun 2020 17:41:13: 19000000 INFO @ Sun, 21 Jun 2020 17:41:16: 11000000 INFO @ Sun, 21 Jun 2020 17:41:17: 14000000 INFO @ Sun, 21 Jun 2020 17:41:20: 20000000 INFO @ Sun, 21 Jun 2020 17:41:23: 12000000 INFO @ Sun, 21 Jun 2020 17:41:23: 15000000 INFO @ Sun, 21 Jun 2020 17:41:27: 21000000 INFO @ Sun, 21 Jun 2020 17:41:29: 13000000 INFO @ Sun, 21 Jun 2020 17:41:30: 16000000 INFO @ Sun, 21 Jun 2020 17:41:34: 22000000 INFO @ Sun, 21 Jun 2020 17:41:35: 14000000 INFO @ Sun, 21 Jun 2020 17:41:37: 17000000 INFO @ Sun, 21 Jun 2020 17:41:42: 15000000 INFO @ Sun, 21 Jun 2020 17:41:42: 23000000 INFO @ Sun, 21 Jun 2020 17:41:43: 18000000 INFO @ Sun, 21 Jun 2020 17:41:48: 16000000 INFO @ Sun, 21 Jun 2020 17:41:49: 24000000 INFO @ Sun, 21 Jun 2020 17:41:50: 19000000 INFO @ Sun, 21 Jun 2020 17:41:54: 17000000 INFO @ Sun, 21 Jun 2020 17:41:56: 25000000 INFO @ Sun, 21 Jun 2020 17:41:57: 20000000 INFO @ Sun, 21 Jun 2020 17:42:01: 18000000 INFO @ Sun, 21 Jun 2020 17:42:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:42:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:42:03: #1 total tags in treatment: 25986467 INFO @ Sun, 21 Jun 2020 17:42:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:42:03: #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 17:42:04: #1 tags after filtering in treatment: 25986443 INFO @ Sun, 21 Jun 2020 17:42:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:42:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:42:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:42:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:42:04: 21000000 INFO @ Sun, 21 Jun 2020 17:42:06: #2 number of paired peaks: 526 WARNING @ Sun, 21 Jun 2020 17:42:06: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Sun, 21 Jun 2020 17:42:06: start model_add_line... INFO @ Sun, 21 Jun 2020 17:42:06: start X-correlation... INFO @ Sun, 21 Jun 2020 17:42:06: end of X-cor INFO @ Sun, 21 Jun 2020 17:42:06: #2 finished! INFO @ Sun, 21 Jun 2020 17:42:06: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 17:42:06: #2 alternative fragment length(s) may be 124 bps INFO @ Sun, 21 Jun 2020 17:42:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.05_model.r INFO @ Sun, 21 Jun 2020 17:42:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:42:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:42:07: 19000000 INFO @ Sun, 21 Jun 2020 17:42:11: 22000000 INFO @ Sun, 21 Jun 2020 17:42:14: 20000000 INFO @ Sun, 21 Jun 2020 17:42:17: 23000000 INFO @ Sun, 21 Jun 2020 17:42:21: 21000000 INFO @ Sun, 21 Jun 2020 17:42:23: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:42:27: 22000000 INFO @ Sun, 21 Jun 2020 17:42:30: 25000000 INFO @ Sun, 21 Jun 2020 17:42:34: 23000000 INFO @ Sun, 21 Jun 2020 17:42:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:42:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:42:36: #1 total tags in treatment: 25986467 INFO @ Sun, 21 Jun 2020 17:42:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:42:36: #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 17:42:37: #1 tags after filtering in treatment: 25986443 INFO @ Sun, 21 Jun 2020 17:42:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:42:37: #1 finished! INFO @ Sun, 21 Jun 2020 17:42:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:42:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:42:39: #2 number of paired peaks: 526 WARNING @ Sun, 21 Jun 2020 17:42:39: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Sun, 21 Jun 2020 17:42:39: start model_add_line... INFO @ Sun, 21 Jun 2020 17:42:39: start X-correlation... INFO @ Sun, 21 Jun 2020 17:42:39: end of X-cor INFO @ Sun, 21 Jun 2020 17:42:39: #2 finished! INFO @ Sun, 21 Jun 2020 17:42:39: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 17:42:39: #2 alternative fragment length(s) may be 124 bps INFO @ Sun, 21 Jun 2020 17:42:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.10_model.r INFO @ Sun, 21 Jun 2020 17:42:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:42:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:42:39: 24000000 INFO @ Sun, 21 Jun 2020 17:42:45: 25000000 INFO @ Sun, 21 Jun 2020 17:42:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:42:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:42:52: #1 total tags in treatment: 25986467 INFO @ Sun, 21 Jun 2020 17:42:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:42:52: #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 17:42:53: #1 tags after filtering in treatment: 25986443 INFO @ Sun, 21 Jun 2020 17:42:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:42:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:42:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:42:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:42:55: #2 number of paired peaks: 526 WARNING @ Sun, 21 Jun 2020 17:42:55: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Sun, 21 Jun 2020 17:42:55: start model_add_line... INFO @ Sun, 21 Jun 2020 17:42:55: start X-correlation... INFO @ Sun, 21 Jun 2020 17:42:55: end of X-cor INFO @ Sun, 21 Jun 2020 17:42:55: #2 finished! INFO @ Sun, 21 Jun 2020 17:42:55: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 17:42:55: #2 alternative fragment length(s) may be 124 bps INFO @ Sun, 21 Jun 2020 17:42:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.20_model.r INFO @ Sun, 21 Jun 2020 17:42:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:42:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:42:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:43:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:43:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:43:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.05_summits.bed INFO @ Sun, 21 Jun 2020 17:43:21: Done! pass1 - making usageList (1079 chroms): 5 millis pass2 - checking and writing primary data (20343 records, 4 fields): 79 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:43:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:43:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:43:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:43:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:43:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.10_summits.bed INFO @ Sun, 21 Jun 2020 17:43:55: Done! pass1 - making usageList (898 chroms): 3 millis pass2 - checking and writing primary data (10342 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:44:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:44:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:44:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032404/SRX1032404.20_summits.bed INFO @ Sun, 21 Jun 2020 17:44:05: Done! pass1 - making usageList (605 chroms): 2 millis pass2 - checking and writing primary data (4771 records, 4 fields): 38 millis CompletedMACS2peakCalling