Job ID = 6453256 SRX = SRX110774 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:12:48 prefetch.2.10.7: 1) Downloading 'SRR388356'... 2020-06-21T08:12:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:15:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:15:20 prefetch.2.10.7: 'SRR388356' is valid 2020-06-21T08:15:20 prefetch.2.10.7: 1) 'SRR388356' was downloaded successfully Read 40289302 spots for SRR388356/SRR388356.sra Written 40289302 spots for SRR388356/SRR388356.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: 00:12:12 40289302 reads; of these: 40289302 (100.00%) were unpaired; of these: 1796459 (4.46%) aligned 0 times 17382616 (43.14%) aligned exactly 1 time 21110227 (52.40%) aligned >1 times 95.54% overall alignment rate Time searching: 00:12:13 Overall time: 00:12:13 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] 16381351 / 38492843 = 0.4256 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 17:34:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.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 17:34:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:45: 1000000 INFO @ Sun, 21 Jun 2020 17:34:50: 2000000 INFO @ Sun, 21 Jun 2020 17:34:54: 3000000 INFO @ Sun, 21 Jun 2020 17:34:58: 4000000 INFO @ Sun, 21 Jun 2020 17:35:03: 5000000 INFO @ Sun, 21 Jun 2020 17:35:07: 6000000 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 17:35:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.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 17:35:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:35:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:35:11: 7000000 INFO @ Sun, 21 Jun 2020 17:35:16: 1000000 INFO @ Sun, 21 Jun 2020 17:35:16: 8000000 INFO @ Sun, 21 Jun 2020 17:35:21: 2000000 INFO @ Sun, 21 Jun 2020 17:35:21: 9000000 INFO @ Sun, 21 Jun 2020 17:35:26: 3000000 INFO @ Sun, 21 Jun 2020 17:35:26: 10000000 INFO @ Sun, 21 Jun 2020 17:35:31: 4000000 INFO @ Sun, 21 Jun 2020 17:35:31: 11000000 INFO @ Sun, 21 Jun 2020 17:35:35: 5000000 INFO @ Sun, 21 Jun 2020 17:35:36: 12000000 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 17:35:40: 6000000 INFO @ Sun, 21 Jun 2020 17:35:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.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 17:35:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:35:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:35:41: 13000000 INFO @ Sun, 21 Jun 2020 17:35:45: 7000000 INFO @ Sun, 21 Jun 2020 17:35:46: 1000000 INFO @ Sun, 21 Jun 2020 17:35:46: 14000000 INFO @ Sun, 21 Jun 2020 17:35:50: 8000000 INFO @ Sun, 21 Jun 2020 17:35:51: 2000000 INFO @ Sun, 21 Jun 2020 17:35:51: 15000000 INFO @ Sun, 21 Jun 2020 17:35:55: 9000000 INFO @ Sun, 21 Jun 2020 17:35:56: 3000000 INFO @ Sun, 21 Jun 2020 17:35:56: 16000000 INFO @ Sun, 21 Jun 2020 17:36:00: 10000000 INFO @ Sun, 21 Jun 2020 17:36:01: 4000000 INFO @ Sun, 21 Jun 2020 17:36:01: 17000000 INFO @ Sun, 21 Jun 2020 17:36:05: 11000000 INFO @ Sun, 21 Jun 2020 17:36:06: 5000000 INFO @ Sun, 21 Jun 2020 17:36:06: 18000000 INFO @ Sun, 21 Jun 2020 17:36:10: 12000000 INFO @ Sun, 21 Jun 2020 17:36:11: 6000000 INFO @ Sun, 21 Jun 2020 17:36:11: 19000000 INFO @ Sun, 21 Jun 2020 17:36:15: 13000000 INFO @ Sun, 21 Jun 2020 17:36:16: 7000000 INFO @ Sun, 21 Jun 2020 17:36:16: 20000000 INFO @ Sun, 21 Jun 2020 17:36:19: 14000000 INFO @ Sun, 21 Jun 2020 17:36:21: 8000000 INFO @ Sun, 21 Jun 2020 17:36:21: 21000000 INFO @ Sun, 21 Jun 2020 17:36:24: 15000000 INFO @ Sun, 21 Jun 2020 17:36:26: 9000000 INFO @ Sun, 21 Jun 2020 17:36:26: 22000000 INFO @ Sun, 21 Jun 2020 17:36:27: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:36:27: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:36:27: #1 total tags in treatment: 22111492 INFO @ Sun, 21 Jun 2020 17:36:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:36:27: #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 17:36:28: #1 tags after filtering in treatment: 22111492 INFO @ Sun, 21 Jun 2020 17:36:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:36:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:36:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:36:29: 16000000 INFO @ Sun, 21 Jun 2020 17:36:29: #2 number of paired peaks: 2900 INFO @ Sun, 21 Jun 2020 17:36:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:36:30: start X-correlation... INFO @ Sun, 21 Jun 2020 17:36:30: end of X-cor INFO @ Sun, 21 Jun 2020 17:36:30: #2 finished! INFO @ Sun, 21 Jun 2020 17:36:30: #2 predicted fragment length is 379 bps INFO @ Sun, 21 Jun 2020 17:36:30: #2 alternative fragment length(s) may be 379 bps INFO @ Sun, 21 Jun 2020 17:36:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.05_model.r INFO @ Sun, 21 Jun 2020 17:36:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:36:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:36:31: 10000000 INFO @ Sun, 21 Jun 2020 17:36:34: 17000000 INFO @ Sun, 21 Jun 2020 17:36:36: 11000000 INFO @ Sun, 21 Jun 2020 17:36:39: 18000000 INFO @ Sun, 21 Jun 2020 17:36:41: 12000000 INFO @ Sun, 21 Jun 2020 17:36:44: 19000000 INFO @ Sun, 21 Jun 2020 17:36:46: 13000000 INFO @ Sun, 21 Jun 2020 17:36:49: 20000000 INFO @ Sun, 21 Jun 2020 17:36:51: 14000000 INFO @ Sun, 21 Jun 2020 17:36:54: 21000000 INFO @ Sun, 21 Jun 2020 17:36:56: 15000000 INFO @ Sun, 21 Jun 2020 17:36:59: 22000000 INFO @ Sun, 21 Jun 2020 17:37:00: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:37:00: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:37:00: #1 total tags in treatment: 22111492 INFO @ Sun, 21 Jun 2020 17:37:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:37:00: #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 17:37:00: #1 tags after filtering in treatment: 22111492 INFO @ Sun, 21 Jun 2020 17:37:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:37:00: #1 finished! INFO @ Sun, 21 Jun 2020 17:37:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:37:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:37:01: 16000000 INFO @ Sun, 21 Jun 2020 17:37:02: #2 number of paired peaks: 2900 INFO @ Sun, 21 Jun 2020 17:37:02: start model_add_line... INFO @ Sun, 21 Jun 2020 17:37:02: start X-correlation... INFO @ Sun, 21 Jun 2020 17:37:02: end of X-cor INFO @ Sun, 21 Jun 2020 17:37:02: #2 finished! INFO @ Sun, 21 Jun 2020 17:37:02: #2 predicted fragment length is 379 bps INFO @ Sun, 21 Jun 2020 17:37:02: #2 alternative fragment length(s) may be 379 bps INFO @ Sun, 21 Jun 2020 17:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.10_model.r INFO @ Sun, 21 Jun 2020 17:37:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:37:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:37:06: 17000000 INFO @ Sun, 21 Jun 2020 17:37:11: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:37:17: 19000000 INFO @ Sun, 21 Jun 2020 17:37:22: 20000000 INFO @ Sun, 21 Jun 2020 17:37:27: 21000000 INFO @ Sun, 21 Jun 2020 17:37:33: 22000000 INFO @ Sun, 21 Jun 2020 17:37:34: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:37:34: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:37:34: #1 total tags in treatment: 22111492 INFO @ Sun, 21 Jun 2020 17:37:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:37:34: #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 17:37:34: #1 tags after filtering in treatment: 22111492 INFO @ Sun, 21 Jun 2020 17:37:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:37:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:37:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:37:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:37:36: #2 number of paired peaks: 2900 INFO @ Sun, 21 Jun 2020 17:37:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:37:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:37:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:37:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:37:36: #2 predicted fragment length is 379 bps INFO @ Sun, 21 Jun 2020 17:37:36: #2 alternative fragment length(s) may be 379 bps INFO @ Sun, 21 Jun 2020 17:37:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.20_model.r INFO @ Sun, 21 Jun 2020 17:37:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:37:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:37:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:38:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.05_summits.bed INFO @ Sun, 21 Jun 2020 17:38:08: Done! pass1 - making usageList (518 chroms): 2 millis pass2 - checking and writing primary data (6660 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:38:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.10_summits.bed INFO @ Sun, 21 Jun 2020 17:38:41: Done! pass1 - making usageList (470 chroms): 1 millis pass2 - checking and writing primary data (5383 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:38:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:39:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:39:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:39:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110774/SRX110774.20_summits.bed INFO @ Sun, 21 Jun 2020 17:39:14: Done! pass1 - making usageList (426 chroms): 2 millis pass2 - checking and writing primary data (4012 records, 4 fields): 16 millis CompletedMACS2peakCalling