Job ID = 6452615 SRX = SRX018629 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:55:00 prefetch.2.10.7: 1) Downloading 'SRR039093'... 2020-06-21T07:55:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:55:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:55:32 prefetch.2.10.7: 'SRR039093' is valid 2020-06-21T07:55:32 prefetch.2.10.7: 1) 'SRR039093' was downloaded successfully Read 4532175 spots for SRR039093/SRR039093.sra Written 4532175 spots for SRR039093/SRR039093.sra 2020-06-21T07:55:55 prefetch.2.10.7: 1) Downloading 'SRR039094'... 2020-06-21T07:55:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:57:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:57:08 prefetch.2.10.7: 'SRR039094' is valid 2020-06-21T07:57:08 prefetch.2.10.7: 1) 'SRR039094' was downloaded successfully Read 5653689 spots for SRR039094/SRR039094.sra Written 5653689 spots for SRR039094/SRR039094.sra 2020-06-21T07:57:37 prefetch.2.10.7: 1) Downloading 'SRR039095'... 2020-06-21T07:57:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:58:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:58:32 prefetch.2.10.7: 'SRR039095' is valid 2020-06-21T07:58:32 prefetch.2.10.7: 1) 'SRR039095' was downloaded successfully Read 4620331 spots for SRR039095/SRR039095.sra Written 4620331 spots for SRR039095/SRR039095.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: 00:02:48 14806195 reads; of these: 14806195 (100.00%) were unpaired; of these: 4704453 (31.77%) aligned 0 times 6958488 (47.00%) aligned exactly 1 time 3143254 (21.23%) aligned >1 times 68.23% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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_rmdupse_core] 1017372 / 10101742 = 0.1007 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 17:04:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.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 17:04:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:04:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:04:42: 1000000 INFO @ Sun, 21 Jun 2020 17:04:48: 2000000 INFO @ Sun, 21 Jun 2020 17:04:54: 3000000 INFO @ Sun, 21 Jun 2020 17:04:59: 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 17:05:05: 5000000 INFO @ Sun, 21 Jun 2020 17:05:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.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 17:05:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:05:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:05:12: 6000000 INFO @ Sun, 21 Jun 2020 17:05:14: 1000000 INFO @ Sun, 21 Jun 2020 17:05:18: 7000000 INFO @ Sun, 21 Jun 2020 17:05:22: 2000000 INFO @ Sun, 21 Jun 2020 17:05:26: 8000000 INFO @ Sun, 21 Jun 2020 17:05:29: 3000000 INFO @ Sun, 21 Jun 2020 17:05:33: 9000000 INFO @ Sun, 21 Jun 2020 17:05:33: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:05:33: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:05:33: #1 total tags in treatment: 9084370 INFO @ Sun, 21 Jun 2020 17:05:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:05:33: #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 17:05:34: #1 tags after filtering in treatment: 9084274 INFO @ Sun, 21 Jun 2020 17:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:05:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:05:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:05:35: #2 number of paired peaks: 1280 INFO @ Sun, 21 Jun 2020 17:05:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:05:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:05:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:05:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:05:35: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 17:05:35: #2 alternative fragment length(s) may be 4,82 bps INFO @ Sun, 21 Jun 2020 17:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.05_model.r INFO @ Sun, 21 Jun 2020 17:05:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:05:35: #3 Pre-compute pvalue-qvalue table... 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 17:05:36: 4000000 INFO @ Sun, 21 Jun 2020 17:05:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.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 17:05:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:05:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:05:43: 5000000 INFO @ Sun, 21 Jun 2020 17:05:44: 1000000 INFO @ Sun, 21 Jun 2020 17:05:50: 6000000 INFO @ Sun, 21 Jun 2020 17:05:52: 2000000 INFO @ Sun, 21 Jun 2020 17:05:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:05:57: 7000000 INFO @ Sun, 21 Jun 2020 17:05:59: 3000000 INFO @ Sun, 21 Jun 2020 17:06:05: 8000000 INFO @ Sun, 21 Jun 2020 17:06:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:06:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:06:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.05_summits.bed INFO @ Sun, 21 Jun 2020 17:06:06: Done! INFO @ Sun, 21 Jun 2020 17:06:06: 4000000 pass1 - making usageList (626 chroms): 1 millis pass2 - checking and writing primary data (3081 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:06:12: 9000000 INFO @ Sun, 21 Jun 2020 17:06:13: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:06:13: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:06:13: #1 total tags in treatment: 9084370 INFO @ Sun, 21 Jun 2020 17:06:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:06:13: #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 17:06:13: #1 tags after filtering in treatment: 9084274 INFO @ Sun, 21 Jun 2020 17:06:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:06:13: #1 finished! INFO @ Sun, 21 Jun 2020 17:06:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:06:13: 5000000 INFO @ Sun, 21 Jun 2020 17:06:14: #2 number of paired peaks: 1280 INFO @ Sun, 21 Jun 2020 17:06:14: start model_add_line... INFO @ Sun, 21 Jun 2020 17:06:14: start X-correlation... INFO @ Sun, 21 Jun 2020 17:06:14: end of X-cor INFO @ Sun, 21 Jun 2020 17:06:14: #2 finished! INFO @ Sun, 21 Jun 2020 17:06:14: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 17:06:14: #2 alternative fragment length(s) may be 4,82 bps INFO @ Sun, 21 Jun 2020 17:06:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.10_model.r INFO @ Sun, 21 Jun 2020 17:06:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:06:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:06:20: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:06:26: 7000000 INFO @ Sun, 21 Jun 2020 17:06:33: 8000000 INFO @ Sun, 21 Jun 2020 17:06:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:06:40: 9000000 INFO @ Sun, 21 Jun 2020 17:06:40: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:06:40: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:06:40: #1 total tags in treatment: 9084370 INFO @ Sun, 21 Jun 2020 17:06:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:06:40: #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 17:06:41: #1 tags after filtering in treatment: 9084274 INFO @ Sun, 21 Jun 2020 17:06:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:06:41: #1 finished! INFO @ Sun, 21 Jun 2020 17:06:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:06:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:06:42: #2 number of paired peaks: 1280 INFO @ Sun, 21 Jun 2020 17:06:42: start model_add_line... INFO @ Sun, 21 Jun 2020 17:06:42: start X-correlation... INFO @ Sun, 21 Jun 2020 17:06:42: end of X-cor INFO @ Sun, 21 Jun 2020 17:06:42: #2 finished! INFO @ Sun, 21 Jun 2020 17:06:42: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 17:06:42: #2 alternative fragment length(s) may be 4,82 bps INFO @ Sun, 21 Jun 2020 17:06:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.20_model.r INFO @ Sun, 21 Jun 2020 17:06:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:06:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:06:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:06:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:06:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.10_summits.bed INFO @ Sun, 21 Jun 2020 17:06:44: Done! pass1 - making usageList (416 chroms): 2 millis pass2 - checking and writing primary data (1356 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:07:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:07:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:07:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:07:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX018629/SRX018629.20_summits.bed INFO @ Sun, 21 Jun 2020 17:07:12: Done! pass1 - making usageList (168 chroms): 1 millis pass2 - checking and writing primary data (532 records, 4 fields): 6 millis CompletedMACS2peakCalling