Job ID = 6457933 SRX = SRX4923180 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:59:51 prefetch.2.10.7: 1) Downloading 'SRR8096330'... 2020-06-21T11:59:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:01:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:01:44 prefetch.2.10.7: 'SRR8096330' is valid 2020-06-21T12:01:44 prefetch.2.10.7: 1) 'SRR8096330' was downloaded successfully 2020-06-21T12:01:44 prefetch.2.10.7: 'SRR8096330' has 0 unresolved dependencies Read 18659061 spots for SRR8096330/SRR8096330.sra Written 18659061 spots for SRR8096330/SRR8096330.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: 00:04:23 18659061 reads; of these: 18659061 (100.00%) were unpaired; of these: 431856 (2.31%) aligned 0 times 14661651 (78.58%) aligned exactly 1 time 3565554 (19.11%) aligned >1 times 97.69% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 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 8 files... [bam_rmdupse_core] 5798567 / 18227205 = 0.3181 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 21:10:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.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 21:10:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:10:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:10:36: 1000000 INFO @ Sun, 21 Jun 2020 21:10:42: 2000000 INFO @ Sun, 21 Jun 2020 21:10:48: 3000000 INFO @ Sun, 21 Jun 2020 21:10:55: 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 21:10:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.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 21:10:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:10:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:11:01: 5000000 INFO @ Sun, 21 Jun 2020 21:11:06: 1000000 INFO @ Sun, 21 Jun 2020 21:11:08: 6000000 INFO @ Sun, 21 Jun 2020 21:11:12: 2000000 INFO @ Sun, 21 Jun 2020 21:11:14: 7000000 INFO @ Sun, 21 Jun 2020 21:11:19: 3000000 INFO @ Sun, 21 Jun 2020 21:11:21: 8000000 INFO @ Sun, 21 Jun 2020 21:11:25: 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 21:11:28: 9000000 INFO @ Sun, 21 Jun 2020 21:11:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.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 21:11:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:11:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:11:31: 5000000 INFO @ Sun, 21 Jun 2020 21:11:35: 10000000 INFO @ Sun, 21 Jun 2020 21:11:36: 1000000 INFO @ Sun, 21 Jun 2020 21:11:38: 6000000 INFO @ Sun, 21 Jun 2020 21:11:42: 11000000 INFO @ Sun, 21 Jun 2020 21:11:43: 2000000 INFO @ Sun, 21 Jun 2020 21:11:44: 7000000 INFO @ Sun, 21 Jun 2020 21:11:48: 12000000 INFO @ Sun, 21 Jun 2020 21:11:49: 3000000 INFO @ Sun, 21 Jun 2020 21:11:50: 8000000 INFO @ Sun, 21 Jun 2020 21:11:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:11:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:11:52: #1 total tags in treatment: 12428638 INFO @ Sun, 21 Jun 2020 21:11:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:11:52: #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 21:11:52: #1 tags after filtering in treatment: 12428520 INFO @ Sun, 21 Jun 2020 21:11:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:11:52: #1 finished! INFO @ Sun, 21 Jun 2020 21:11:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:11:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:11:53: #2 number of paired peaks: 8119 INFO @ Sun, 21 Jun 2020 21:11:53: start model_add_line... INFO @ Sun, 21 Jun 2020 21:11:54: start X-correlation... INFO @ Sun, 21 Jun 2020 21:11:54: end of X-cor INFO @ Sun, 21 Jun 2020 21:11:54: #2 finished! INFO @ Sun, 21 Jun 2020 21:11:54: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:11:54: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:11:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.05_model.r INFO @ Sun, 21 Jun 2020 21:11:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:11:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:11:56: 4000000 INFO @ Sun, 21 Jun 2020 21:11:56: 9000000 INFO @ Sun, 21 Jun 2020 21:12:02: 5000000 INFO @ Sun, 21 Jun 2020 21:12:03: 10000000 INFO @ Sun, 21 Jun 2020 21:12:08: 6000000 INFO @ Sun, 21 Jun 2020 21:12:09: 11000000 INFO @ Sun, 21 Jun 2020 21:12:14: 7000000 INFO @ Sun, 21 Jun 2020 21:12:16: 12000000 INFO @ Sun, 21 Jun 2020 21:12:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:12:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:12:19: #1 total tags in treatment: 12428638 INFO @ Sun, 21 Jun 2020 21:12:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:12:19: #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 21:12:19: #1 tags after filtering in treatment: 12428520 INFO @ Sun, 21 Jun 2020 21:12:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:12:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:12:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:12:20: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:12:20: #2 number of paired peaks: 8119 INFO @ Sun, 21 Jun 2020 21:12:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:12:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:12:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:12:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:12:21: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:12:21: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:12:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.10_model.r INFO @ Sun, 21 Jun 2020 21:12:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:12:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:12:26: 9000000 INFO @ Sun, 21 Jun 2020 21:12:32: 10000000 INFO @ Sun, 21 Jun 2020 21:12:37: 11000000 INFO @ Sun, 21 Jun 2020 21:12:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:12:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:12:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.05_summits.bed INFO @ Sun, 21 Jun 2020 21:12:39: Done! pass1 - making usageList (598 chroms): 2 millis pass2 - checking and writing primary data (9846 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:12:43: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:12:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:12:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:12:45: #1 total tags in treatment: 12428638 INFO @ Sun, 21 Jun 2020 21:12:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:12:45: #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 21:12:46: #1 tags after filtering in treatment: 12428520 INFO @ Sun, 21 Jun 2020 21:12:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:12:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:12:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:12:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:12:47: #2 number of paired peaks: 8119 INFO @ Sun, 21 Jun 2020 21:12:47: start model_add_line... INFO @ Sun, 21 Jun 2020 21:12:47: start X-correlation... INFO @ Sun, 21 Jun 2020 21:12:47: end of X-cor INFO @ Sun, 21 Jun 2020 21:12:47: #2 finished! INFO @ Sun, 21 Jun 2020 21:12:47: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:12:47: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:12:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.20_model.r INFO @ Sun, 21 Jun 2020 21:12:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:12:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:12:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:13:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:13:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:13:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.10_summits.bed INFO @ Sun, 21 Jun 2020 21:13:06: Done! pass1 - making usageList (517 chroms): 2 millis pass2 - checking and writing primary data (8656 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:13:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:13:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:13:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923180/SRX4923180.20_summits.bed INFO @ Sun, 21 Jun 2020 21:13:30: Done! pass1 - making usageList (360 chroms): 2 millis pass2 - checking and writing primary data (6787 records, 4 fields): 18 millis CompletedMACS2peakCalling