Job ID = 6457940 SRX = SRX4923184 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:06:39 prefetch.2.10.7: 1) Downloading 'SRR8096334'... 2020-06-21T12:06:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:08:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:08:15 prefetch.2.10.7: 'SRR8096334' is valid 2020-06-21T12:08:15 prefetch.2.10.7: 1) 'SRR8096334' was downloaded successfully 2020-06-21T12:08:15 prefetch.2.10.7: 'SRR8096334' has 0 unresolved dependencies Read 20720028 spots for SRR8096334/SRR8096334.sra Written 20720028 spots for SRR8096334/SRR8096334.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:51 20720028 reads; of these: 20720028 (100.00%) were unpaired; of these: 468305 (2.26%) aligned 0 times 16524964 (79.75%) aligned exactly 1 time 3726759 (17.99%) aligned >1 times 97.74% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 6951350 / 20251723 = 0.3432 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 21:18:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.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 21:18:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:18:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:18:56: 1000000 INFO @ Sun, 21 Jun 2020 21:19:01: 2000000 INFO @ Sun, 21 Jun 2020 21:19:07: 3000000 INFO @ Sun, 21 Jun 2020 21:19:12: 4000000 INFO @ Sun, 21 Jun 2020 21:19:17: 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 21:19:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.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 21:19:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:19:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:19:23: 6000000 INFO @ Sun, 21 Jun 2020 21:19:25: 1000000 INFO @ Sun, 21 Jun 2020 21:19:28: 7000000 INFO @ Sun, 21 Jun 2020 21:19:31: 2000000 INFO @ Sun, 21 Jun 2020 21:19:34: 8000000 INFO @ Sun, 21 Jun 2020 21:19:36: 3000000 INFO @ Sun, 21 Jun 2020 21:19:39: 9000000 INFO @ Sun, 21 Jun 2020 21:19:41: 4000000 INFO @ Sun, 21 Jun 2020 21:19:45: 10000000 INFO @ Sun, 21 Jun 2020 21:19:47: 5000000 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 21:19:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.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 21:19:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:19:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:19:51: 11000000 INFO @ Sun, 21 Jun 2020 21:19:52: 6000000 INFO @ Sun, 21 Jun 2020 21:19:56: 1000000 INFO @ Sun, 21 Jun 2020 21:19:57: 12000000 INFO @ Sun, 21 Jun 2020 21:19:58: 7000000 INFO @ Sun, 21 Jun 2020 21:20:02: 2000000 INFO @ Sun, 21 Jun 2020 21:20:02: 13000000 INFO @ Sun, 21 Jun 2020 21:20:04: 8000000 INFO @ Sun, 21 Jun 2020 21:20:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:20:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:20:04: #1 total tags in treatment: 13300373 INFO @ Sun, 21 Jun 2020 21:20:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:20:04: #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 21:20:05: #1 tags after filtering in treatment: 13300274 INFO @ Sun, 21 Jun 2020 21:20:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:20:05: #1 finished! INFO @ Sun, 21 Jun 2020 21:20:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:20:07: #2 number of paired peaks: 9196 INFO @ Sun, 21 Jun 2020 21:20:07: start model_add_line... INFO @ Sun, 21 Jun 2020 21:20:07: start X-correlation... INFO @ Sun, 21 Jun 2020 21:20:07: end of X-cor INFO @ Sun, 21 Jun 2020 21:20:07: #2 finished! INFO @ Sun, 21 Jun 2020 21:20:07: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 21:20:07: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 21:20:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.05_model.r INFO @ Sun, 21 Jun 2020 21:20:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:20:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:20:08: 3000000 INFO @ Sun, 21 Jun 2020 21:20:10: 9000000 INFO @ Sun, 21 Jun 2020 21:20:14: 4000000 INFO @ Sun, 21 Jun 2020 21:20:16: 10000000 INFO @ Sun, 21 Jun 2020 21:20:20: 5000000 INFO @ Sun, 21 Jun 2020 21:20:22: 11000000 INFO @ Sun, 21 Jun 2020 21:20:26: 6000000 INFO @ Sun, 21 Jun 2020 21:20:28: 12000000 INFO @ Sun, 21 Jun 2020 21:20:31: 7000000 INFO @ Sun, 21 Jun 2020 21:20:34: 13000000 INFO @ Sun, 21 Jun 2020 21:20:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:20:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:20:37: #1 total tags in treatment: 13300373 INFO @ Sun, 21 Jun 2020 21:20:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:20:37: #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 21:20:37: #1 tags after filtering in treatment: 13300274 INFO @ Sun, 21 Jun 2020 21:20:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:20:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:20:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:20:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:20:37: 8000000 INFO @ Sun, 21 Jun 2020 21:20:39: #2 number of paired peaks: 9196 INFO @ Sun, 21 Jun 2020 21:20:39: start model_add_line... INFO @ Sun, 21 Jun 2020 21:20:39: start X-correlation... INFO @ Sun, 21 Jun 2020 21:20:39: end of X-cor INFO @ Sun, 21 Jun 2020 21:20:39: #2 finished! INFO @ Sun, 21 Jun 2020 21:20:39: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 21:20:39: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 21:20:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.10_model.r INFO @ Sun, 21 Jun 2020 21:20:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:20:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:20:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:20:43: 9000000 INFO @ Sun, 21 Jun 2020 21:20:48: 10000000 INFO @ Sun, 21 Jun 2020 21:20:54: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:20:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:20:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:20:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.05_summits.bed INFO @ Sun, 21 Jun 2020 21:20:56: Done! pass1 - making usageList (593 chroms): 3 millis pass2 - checking and writing primary data (10421 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:20:59: 12000000 INFO @ Sun, 21 Jun 2020 21:21:04: 13000000 INFO @ Sun, 21 Jun 2020 21:21:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:21:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:21:06: #1 total tags in treatment: 13300373 INFO @ Sun, 21 Jun 2020 21:21:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:06: #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 21:21:07: #1 tags after filtering in treatment: 13300274 INFO @ Sun, 21 Jun 2020 21:21:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:09: #2 number of paired peaks: 9196 INFO @ Sun, 21 Jun 2020 21:21:09: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:09: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:09: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:09: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:09: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 21:21:09: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 21:21:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.20_model.r INFO @ Sun, 21 Jun 2020 21:21:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:21:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:21:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:21:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:21:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.10_summits.bed INFO @ Sun, 21 Jun 2020 21:21:27: Done! pass1 - making usageList (504 chroms): 3 millis pass2 - checking and writing primary data (9076 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:21:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:21:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:21:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:21:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923184/SRX4923184.20_summits.bed INFO @ Sun, 21 Jun 2020 21:21:57: Done! pass1 - making usageList (282 chroms): 2 millis pass2 - checking and writing primary data (6982 records, 4 fields): 26 millis CompletedMACS2peakCalling