Job ID = 6452646 SRX = SRX022335 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:54:45 prefetch.2.10.7: 1) Downloading 'SRR058396'... 2020-06-21T07:54:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:56:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:56:01 prefetch.2.10.7: 'SRR058396' is valid 2020-06-21T07:56:01 prefetch.2.10.7: 1) 'SRR058396' was downloaded successfully Read 25332619 spots for SRR058396/SRR058396.sra Written 25332619 spots for SRR058396/SRR058396.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: 00:00:01 Multiseed full-index search: 00:04:22 25332619 reads; of these: 25332619 (100.00%) were unpaired; of these: 9009225 (35.56%) aligned 0 times 9091249 (35.89%) aligned exactly 1 time 7232145 (28.55%) aligned >1 times 64.44% 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] 4058736 / 16323394 = 0.2486 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 17:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.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 17:04:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:04:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:04:27: 1000000 INFO @ Sun, 21 Jun 2020 17:04:32: 2000000 INFO @ Sun, 21 Jun 2020 17:04:37: 3000000 INFO @ Sun, 21 Jun 2020 17:04:42: 4000000 INFO @ Sun, 21 Jun 2020 17:04:47: 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 17:04:51: 6000000 INFO @ Sun, 21 Jun 2020 17:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.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 17:04:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:04:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:04:57: 7000000 INFO @ Sun, 21 Jun 2020 17:04:58: 1000000 INFO @ Sun, 21 Jun 2020 17:05:03: 8000000 INFO @ Sun, 21 Jun 2020 17:05:04: 2000000 INFO @ Sun, 21 Jun 2020 17:05:09: 9000000 INFO @ Sun, 21 Jun 2020 17:05:10: 3000000 INFO @ Sun, 21 Jun 2020 17:05:15: 10000000 INFO @ Sun, 21 Jun 2020 17:05:17: 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 17:05:21: 11000000 INFO @ Sun, 21 Jun 2020 17:05:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.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 17:05:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:05:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:05:23: 5000000 INFO @ Sun, 21 Jun 2020 17:05:27: 12000000 INFO @ Sun, 21 Jun 2020 17:05:28: 1000000 INFO @ Sun, 21 Jun 2020 17:05:28: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 17:05:28: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 17:05:28: #1 total tags in treatment: 12264658 INFO @ Sun, 21 Jun 2020 17:05:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:05:28: #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 17:05:29: #1 tags after filtering in treatment: 12264637 INFO @ Sun, 21 Jun 2020 17:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:05:29: #1 finished! INFO @ Sun, 21 Jun 2020 17:05:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:05:29: 6000000 INFO @ Sun, 21 Jun 2020 17:05:30: #2 number of paired peaks: 1610 INFO @ Sun, 21 Jun 2020 17:05:30: start model_add_line... INFO @ Sun, 21 Jun 2020 17:05:30: start X-correlation... INFO @ Sun, 21 Jun 2020 17:05:30: end of X-cor INFO @ Sun, 21 Jun 2020 17:05:30: #2 finished! INFO @ Sun, 21 Jun 2020 17:05:30: #2 predicted fragment length is 89 bps INFO @ Sun, 21 Jun 2020 17:05:30: #2 alternative fragment length(s) may be 3,67,89 bps INFO @ Sun, 21 Jun 2020 17:05:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.05_model.r INFO @ Sun, 21 Jun 2020 17:05:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:05:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:05:33: 2000000 INFO @ Sun, 21 Jun 2020 17:05:36: 7000000 INFO @ Sun, 21 Jun 2020 17:05:40: 3000000 INFO @ Sun, 21 Jun 2020 17:05:42: 8000000 INFO @ Sun, 21 Jun 2020 17:05:46: 4000000 INFO @ Sun, 21 Jun 2020 17:05:48: 9000000 INFO @ Sun, 21 Jun 2020 17:05:52: 5000000 INFO @ Sun, 21 Jun 2020 17:05:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:05:55: 10000000 INFO @ Sun, 21 Jun 2020 17:05:59: 6000000 INFO @ Sun, 21 Jun 2020 17:06:01: 11000000 INFO @ Sun, 21 Jun 2020 17:06:05: 7000000 INFO @ Sun, 21 Jun 2020 17:06:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:06:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:06:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.05_summits.bed INFO @ Sun, 21 Jun 2020 17:06:07: Done! pass1 - making usageList (914 chroms): 2 millis pass2 - checking and writing primary data (8620 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:06:08: 12000000 INFO @ Sun, 21 Jun 2020 17:06:09: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 17:06:09: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 17:06:09: #1 total tags in treatment: 12264658 INFO @ Sun, 21 Jun 2020 17:06:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:06:09: #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 17:06:10: #1 tags after filtering in treatment: 12264637 INFO @ Sun, 21 Jun 2020 17:06:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:06:10: #1 finished! INFO @ Sun, 21 Jun 2020 17:06:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:06:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:06:11: #2 number of paired peaks: 1610 INFO @ Sun, 21 Jun 2020 17:06:11: start model_add_line... INFO @ Sun, 21 Jun 2020 17:06:11: start X-correlation... INFO @ Sun, 21 Jun 2020 17:06:11: end of X-cor INFO @ Sun, 21 Jun 2020 17:06:11: #2 finished! INFO @ Sun, 21 Jun 2020 17:06:11: #2 predicted fragment length is 89 bps INFO @ Sun, 21 Jun 2020 17:06:11: #2 alternative fragment length(s) may be 3,67,89 bps INFO @ Sun, 21 Jun 2020 17:06:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.10_model.r INFO @ Sun, 21 Jun 2020 17:06:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:06:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:06:11: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:06:17: 9000000 INFO @ Sun, 21 Jun 2020 17:06:23: 10000000 INFO @ Sun, 21 Jun 2020 17:06:29: 11000000 INFO @ Sun, 21 Jun 2020 17:06:35: 12000000 INFO @ Sun, 21 Jun 2020 17:06:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:06:36: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 17:06:36: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 17:06:36: #1 total tags in treatment: 12264658 INFO @ Sun, 21 Jun 2020 17:06:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:06:36: #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 17:06:37: #1 tags after filtering in treatment: 12264637 INFO @ Sun, 21 Jun 2020 17:06:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:06:37: #1 finished! INFO @ Sun, 21 Jun 2020 17:06:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:06:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:06:38: #2 number of paired peaks: 1610 INFO @ Sun, 21 Jun 2020 17:06:38: start model_add_line... INFO @ Sun, 21 Jun 2020 17:06:38: start X-correlation... INFO @ Sun, 21 Jun 2020 17:06:38: end of X-cor INFO @ Sun, 21 Jun 2020 17:06:38: #2 finished! INFO @ Sun, 21 Jun 2020 17:06:38: #2 predicted fragment length is 89 bps INFO @ Sun, 21 Jun 2020 17:06:38: #2 alternative fragment length(s) may be 3,67,89 bps INFO @ Sun, 21 Jun 2020 17:06:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.20_model.r INFO @ Sun, 21 Jun 2020 17:06:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:06:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:06:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:06:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:06:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.10_summits.bed INFO @ Sun, 21 Jun 2020 17:06:48: Done! pass1 - making usageList (484 chroms): 1 millis pass2 - checking and writing primary data (2425 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:07:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:07:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:07:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX022335/SRX022335.20_summits.bed INFO @ Sun, 21 Jun 2020 17:07:17: Done! pass1 - making usageList (259 chroms): 1 millis pass2 - checking and writing primary data (765 records, 4 fields): 8 millis CompletedMACS2peakCalling