Job ID = 6454955 SRX = SRX2618498 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:25 prefetch.2.10.7: 1) Downloading 'SRR5319052'... 2020-06-21T09:48:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:51:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:51:05 prefetch.2.10.7: 'SRR5319052' is valid 2020-06-21T09:51:05 prefetch.2.10.7: 1) 'SRR5319052' was downloaded successfully 2020-06-21T09:51:05 prefetch.2.10.7: 'SRR5319052' has 0 unresolved dependencies Read 22654160 spots for SRR5319052/SRR5319052.sra Written 22654160 spots for SRR5319052/SRR5319052.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: 00:04:06 22654160 reads; of these: 22654160 (100.00%) were unpaired; of these: 7565233 (33.39%) aligned 0 times 14029964 (61.93%) aligned exactly 1 time 1058963 (4.67%) aligned >1 times 66.61% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 1956583 / 15088927 = 0.1297 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 19:00:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.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 19:00:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:22: 1000000 INFO @ Sun, 21 Jun 2020 19:00:28: 2000000 INFO @ Sun, 21 Jun 2020 19:00:34: 3000000 INFO @ Sun, 21 Jun 2020 19:00:40: 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 19:00:45: 5000000 INFO @ Sun, 21 Jun 2020 19:00:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.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 19:00:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:51: 6000000 INFO @ Sun, 21 Jun 2020 19:00:52: 1000000 INFO @ Sun, 21 Jun 2020 19:00:57: 7000000 INFO @ Sun, 21 Jun 2020 19:00:58: 2000000 INFO @ Sun, 21 Jun 2020 19:01:03: 8000000 INFO @ Sun, 21 Jun 2020 19:01:05: 3000000 INFO @ Sun, 21 Jun 2020 19:01:09: 9000000 INFO @ Sun, 21 Jun 2020 19:01:10: 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 19:01:15: 10000000 INFO @ Sun, 21 Jun 2020 19:01:16: 5000000 INFO @ Sun, 21 Jun 2020 19:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.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 19:01:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:22: 11000000 INFO @ Sun, 21 Jun 2020 19:01:22: 6000000 INFO @ Sun, 21 Jun 2020 19:01:23: 1000000 INFO @ Sun, 21 Jun 2020 19:01:28: 12000000 INFO @ Sun, 21 Jun 2020 19:01:29: 7000000 INFO @ Sun, 21 Jun 2020 19:01:30: 2000000 INFO @ Sun, 21 Jun 2020 19:01:34: 13000000 INFO @ Sun, 21 Jun 2020 19:01:35: 8000000 INFO @ Sun, 21 Jun 2020 19:01:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:01:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:01:36: #1 total tags in treatment: 13132344 INFO @ Sun, 21 Jun 2020 19:01:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:36: #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 19:01:36: #1 tags after filtering in treatment: 13132248 INFO @ Sun, 21 Jun 2020 19:01:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:01:37: 3000000 INFO @ Sun, 21 Jun 2020 19:01:37: #2 number of paired peaks: 3093 INFO @ Sun, 21 Jun 2020 19:01:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:37: #2 predicted fragment length is 167 bps INFO @ Sun, 21 Jun 2020 19:01:37: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 21 Jun 2020 19:01:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.05_model.r INFO @ Sun, 21 Jun 2020 19:01:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:41: 9000000 INFO @ Sun, 21 Jun 2020 19:01:44: 4000000 INFO @ Sun, 21 Jun 2020 19:01:47: 10000000 INFO @ Sun, 21 Jun 2020 19:01:50: 5000000 INFO @ Sun, 21 Jun 2020 19:01:53: 11000000 INFO @ Sun, 21 Jun 2020 19:01:57: 6000000 INFO @ Sun, 21 Jun 2020 19:01:59: 12000000 INFO @ Sun, 21 Jun 2020 19:02:04: 7000000 INFO @ Sun, 21 Jun 2020 19:02:06: 13000000 INFO @ Sun, 21 Jun 2020 19:02:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:02:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:02:07: #1 total tags in treatment: 13132344 INFO @ Sun, 21 Jun 2020 19:02:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:07: #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 19:02:07: #1 tags after filtering in treatment: 13132248 INFO @ Sun, 21 Jun 2020 19:02:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:08: #2 number of paired peaks: 3093 INFO @ Sun, 21 Jun 2020 19:02:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:08: #2 predicted fragment length is 167 bps INFO @ Sun, 21 Jun 2020 19:02:08: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 21 Jun 2020 19:02:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.10_model.r INFO @ Sun, 21 Jun 2020 19:02:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:10: 8000000 INFO @ Sun, 21 Jun 2020 19:02:12: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:02:17: 9000000 INFO @ Sun, 21 Jun 2020 19:02:23: 10000000 INFO @ Sun, 21 Jun 2020 19:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.05_summits.bed INFO @ Sun, 21 Jun 2020 19:02:29: Done! INFO @ Sun, 21 Jun 2020 19:02:30: 11000000 pass1 - making usageList (224 chroms): 2 millis pass2 - checking and writing primary data (10601 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:02:36: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:02:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:43: 13000000 INFO @ Sun, 21 Jun 2020 19:02:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:02:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:02:44: #1 total tags in treatment: 13132344 INFO @ Sun, 21 Jun 2020 19:02:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:44: #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 19:02:44: #1 tags after filtering in treatment: 13132248 INFO @ Sun, 21 Jun 2020 19:02:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:45: #2 number of paired peaks: 3093 INFO @ Sun, 21 Jun 2020 19:02:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:46: #2 predicted fragment length is 167 bps INFO @ Sun, 21 Jun 2020 19:02:46: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 21 Jun 2020 19:02:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.20_model.r INFO @ Sun, 21 Jun 2020 19:02:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.10_summits.bed INFO @ Sun, 21 Jun 2020 19:03:00: Done! pass1 - making usageList (103 chroms): 2 millis pass2 - checking and writing primary data (7203 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:03:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618498/SRX2618498.20_summits.bed INFO @ Sun, 21 Jun 2020 19:03:34: Done! pass1 - making usageList (58 chroms): 2 millis pass2 - checking and writing primary data (3776 records, 4 fields): 7 millis CompletedMACS2peakCalling