Job ID = 6453082 SRX = SRX1032392 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:59:23 prefetch.2.10.7: 1) Downloading 'SRR2031890'... 2020-06-21T07:59:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:07:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:07:32 prefetch.2.10.7: 1) 'SRR2031890' was downloaded successfully Read 28099620 spots for SRR2031890/SRR2031890.sra Written 28099620 spots for SRR2031890/SRR2031890.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: 00:06:46 28099620 reads; of these: 28099620 (100.00%) were unpaired; of these: 1028823 (3.66%) aligned 0 times 21704345 (77.24%) aligned exactly 1 time 5366452 (19.10%) aligned >1 times 96.34% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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] 7616540 / 27070797 = 0.2814 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 17:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.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 17:22:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:08: 1000000 INFO @ Sun, 21 Jun 2020 17:22:13: 2000000 INFO @ Sun, 21 Jun 2020 17:22:19: 3000000 INFO @ Sun, 21 Jun 2020 17:22:24: 4000000 INFO @ Sun, 21 Jun 2020 17:22:30: 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 17:22:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.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 17:22:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:35: 6000000 INFO @ Sun, 21 Jun 2020 17:22:40: 1000000 INFO @ Sun, 21 Jun 2020 17:22:42: 7000000 INFO @ Sun, 21 Jun 2020 17:22:47: 2000000 INFO @ Sun, 21 Jun 2020 17:22:49: 8000000 INFO @ Sun, 21 Jun 2020 17:22:55: 3000000 INFO @ Sun, 21 Jun 2020 17:22:55: 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 17:23:01: 10000000 INFO @ Sun, 21 Jun 2020 17:23:02: 4000000 INFO @ Sun, 21 Jun 2020 17:23:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.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 17:23:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:08: 11000000 INFO @ Sun, 21 Jun 2020 17:23:09: 1000000 INFO @ Sun, 21 Jun 2020 17:23:10: 5000000 INFO @ Sun, 21 Jun 2020 17:23:15: 12000000 INFO @ Sun, 21 Jun 2020 17:23:17: 2000000 INFO @ Sun, 21 Jun 2020 17:23:17: 6000000 INFO @ Sun, 21 Jun 2020 17:23:21: 13000000 INFO @ Sun, 21 Jun 2020 17:23:24: 3000000 INFO @ Sun, 21 Jun 2020 17:23:25: 7000000 INFO @ Sun, 21 Jun 2020 17:23:28: 14000000 INFO @ Sun, 21 Jun 2020 17:23:31: 4000000 INFO @ Sun, 21 Jun 2020 17:23:32: 8000000 INFO @ Sun, 21 Jun 2020 17:23:35: 15000000 INFO @ Sun, 21 Jun 2020 17:23:38: 5000000 INFO @ Sun, 21 Jun 2020 17:23:39: 9000000 INFO @ Sun, 21 Jun 2020 17:23:42: 16000000 INFO @ Sun, 21 Jun 2020 17:23:45: 6000000 INFO @ Sun, 21 Jun 2020 17:23:47: 10000000 INFO @ Sun, 21 Jun 2020 17:23:48: 17000000 INFO @ Sun, 21 Jun 2020 17:23:53: 7000000 INFO @ Sun, 21 Jun 2020 17:23:54: 11000000 INFO @ Sun, 21 Jun 2020 17:23:55: 18000000 INFO @ Sun, 21 Jun 2020 17:24:00: 8000000 INFO @ Sun, 21 Jun 2020 17:24:02: 12000000 INFO @ Sun, 21 Jun 2020 17:24:02: 19000000 INFO @ Sun, 21 Jun 2020 17:24:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:24:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:24:05: #1 total tags in treatment: 19454257 INFO @ Sun, 21 Jun 2020 17:24:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:05: #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 17:24:06: #1 tags after filtering in treatment: 19454254 INFO @ Sun, 21 Jun 2020 17:24:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:24:06: #1 finished! INFO @ Sun, 21 Jun 2020 17:24:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:24:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:24:07: 9000000 INFO @ Sun, 21 Jun 2020 17:24:07: #2 number of paired peaks: 4167 INFO @ Sun, 21 Jun 2020 17:24:07: start model_add_line... INFO @ Sun, 21 Jun 2020 17:24:07: start X-correlation... INFO @ Sun, 21 Jun 2020 17:24:07: end of X-cor INFO @ Sun, 21 Jun 2020 17:24:07: #2 finished! INFO @ Sun, 21 Jun 2020 17:24:07: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 17:24:07: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sun, 21 Jun 2020 17:24:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.05_model.r INFO @ Sun, 21 Jun 2020 17:24:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:24:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:24:09: 13000000 INFO @ Sun, 21 Jun 2020 17:24:14: 10000000 INFO @ Sun, 21 Jun 2020 17:24:16: 14000000 INFO @ Sun, 21 Jun 2020 17:24:21: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:24:23: 15000000 INFO @ Sun, 21 Jun 2020 17:24:28: 12000000 INFO @ Sun, 21 Jun 2020 17:24:31: 16000000 INFO @ Sun, 21 Jun 2020 17:24:35: 13000000 INFO @ Sun, 21 Jun 2020 17:24:38: 17000000 INFO @ Sun, 21 Jun 2020 17:24:42: 14000000 INFO @ Sun, 21 Jun 2020 17:24:46: 18000000 INFO @ Sun, 21 Jun 2020 17:24:49: 15000000 INFO @ Sun, 21 Jun 2020 17:24:54: 19000000 INFO @ Sun, 21 Jun 2020 17:24:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:56: 16000000 INFO @ Sun, 21 Jun 2020 17:24:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:24:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:24:57: #1 total tags in treatment: 19454257 INFO @ Sun, 21 Jun 2020 17:24:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:57: #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 17:24:58: #1 tags after filtering in treatment: 19454254 INFO @ Sun, 21 Jun 2020 17:24:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:24:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:24:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:24:58: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:25:00: #2 number of paired peaks: 4167 INFO @ Sun, 21 Jun 2020 17:25:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:25:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:25:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:25:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:25:00: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 17:25:00: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sun, 21 Jun 2020 17:25:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.10_model.r INFO @ Sun, 21 Jun 2020 17:25:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:25:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:25:03: 17000000 INFO @ Sun, 21 Jun 2020 17:25:10: 18000000 INFO @ Sun, 21 Jun 2020 17:25:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:25:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:25:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.05_summits.bed INFO @ Sun, 21 Jun 2020 17:25:15: Done! pass1 - making usageList (614 chroms): 2 millis pass2 - checking and writing primary data (6749 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:25:17: 19000000 INFO @ Sun, 21 Jun 2020 17:25:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:25:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:25:20: #1 total tags in treatment: 19454257 INFO @ Sun, 21 Jun 2020 17:25:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:25:20: #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 17:25:20: #1 tags after filtering in treatment: 19454254 INFO @ Sun, 21 Jun 2020 17:25:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:25:20: #1 finished! INFO @ Sun, 21 Jun 2020 17:25:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:25:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:25:22: #2 number of paired peaks: 4167 INFO @ Sun, 21 Jun 2020 17:25:22: start model_add_line... INFO @ Sun, 21 Jun 2020 17:25:22: start X-correlation... INFO @ Sun, 21 Jun 2020 17:25:22: end of X-cor INFO @ Sun, 21 Jun 2020 17:25:22: #2 finished! INFO @ Sun, 21 Jun 2020 17:25:22: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 17:25:22: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sun, 21 Jun 2020 17:25:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.20_model.r INFO @ Sun, 21 Jun 2020 17:25:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:25:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:26:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:26:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.10_summits.bed INFO @ Sun, 21 Jun 2020 17:26:07: Done! pass1 - making usageList (409 chroms): 1 millis pass2 - checking and writing primary data (2644 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:26:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032392/SRX1032392.20_summits.bed INFO @ Sun, 21 Jun 2020 17:26:29: Done! pass1 - making usageList (269 chroms): 1 millis pass2 - checking and writing primary data (896 records, 4 fields): 9 millis CompletedMACS2peakCalling