Job ID = 6498303 SRX = SRX467114 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:16:40 prefetch.2.10.7: 1) Downloading 'SRR1164538'... 2020-06-25T23:16:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:19:04 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:19:05 prefetch.2.10.7: 'SRR1164538' is valid 2020-06-25T23:19:05 prefetch.2.10.7: 1) 'SRR1164538' was downloaded successfully Read 14415791 spots for SRR1164538/SRR1164538.sra Written 14415791 spots for SRR1164538/SRR1164538.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: 00:03:48 14415791 reads; of these: 14415791 (100.00%) were unpaired; of these: 1002991 (6.96%) aligned 0 times 10394557 (72.11%) aligned exactly 1 time 3018243 (20.94%) aligned >1 times 93.04% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1203774 / 13412800 = 0.0897 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 @ Fri, 26 Jun 2020 08:28:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.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 @ Fri, 26 Jun 2020 08:28:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:28:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:28:41: 1000000 INFO @ Fri, 26 Jun 2020 08:28:46: 2000000 INFO @ Fri, 26 Jun 2020 08:28:51: 3000000 INFO @ Fri, 26 Jun 2020 08:28:55: 4000000 INFO @ Fri, 26 Jun 2020 08:29:00: 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 @ Fri, 26 Jun 2020 08:29:05: 6000000 INFO @ Fri, 26 Jun 2020 08:29:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.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 @ Fri, 26 Jun 2020 08:29:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:29:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:29:11: 7000000 INFO @ Fri, 26 Jun 2020 08:29:11: 1000000 INFO @ Fri, 26 Jun 2020 08:29:16: 8000000 INFO @ Fri, 26 Jun 2020 08:29:17: 2000000 INFO @ Fri, 26 Jun 2020 08:29:22: 9000000 INFO @ Fri, 26 Jun 2020 08:29:22: 3000000 INFO @ Fri, 26 Jun 2020 08:29:27: 10000000 INFO @ Fri, 26 Jun 2020 08:29:27: 4000000 INFO @ Fri, 26 Jun 2020 08:29:32: 11000000 INFO @ Fri, 26 Jun 2020 08:29:33: 5000000 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 @ Fri, 26 Jun 2020 08:29:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.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 @ Fri, 26 Jun 2020 08:29:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:29:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:29:38: 12000000 INFO @ Fri, 26 Jun 2020 08:29:38: 6000000 INFO @ Fri, 26 Jun 2020 08:29:39: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:29:39: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:29:39: #1 total tags in treatment: 12209026 INFO @ Fri, 26 Jun 2020 08:29:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:29:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:29:39: #1 tags after filtering in treatment: 12209026 INFO @ Fri, 26 Jun 2020 08:29:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:29:39: #1 finished! INFO @ Fri, 26 Jun 2020 08:29:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:29:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:29:40: #2 number of paired peaks: 2137 INFO @ Fri, 26 Jun 2020 08:29:40: start model_add_line... INFO @ Fri, 26 Jun 2020 08:29:40: start X-correlation... INFO @ Fri, 26 Jun 2020 08:29:40: end of X-cor INFO @ Fri, 26 Jun 2020 08:29:40: #2 finished! INFO @ Fri, 26 Jun 2020 08:29:40: #2 predicted fragment length is 201 bps INFO @ Fri, 26 Jun 2020 08:29:40: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 26 Jun 2020 08:29:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.05_model.r INFO @ Fri, 26 Jun 2020 08:29:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:29:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:29:41: 1000000 INFO @ Fri, 26 Jun 2020 08:29:43: 7000000 INFO @ Fri, 26 Jun 2020 08:29:46: 2000000 INFO @ Fri, 26 Jun 2020 08:29:48: 8000000 INFO @ Fri, 26 Jun 2020 08:29:51: 3000000 INFO @ Fri, 26 Jun 2020 08:29:53: 9000000 INFO @ Fri, 26 Jun 2020 08:29:56: 4000000 INFO @ Fri, 26 Jun 2020 08:29:58: 10000000 INFO @ Fri, 26 Jun 2020 08:30:01: 5000000 INFO @ Fri, 26 Jun 2020 08:30:03: 11000000 INFO @ Fri, 26 Jun 2020 08:30:07: 6000000 INFO @ Fri, 26 Jun 2020 08:30:09: 12000000 INFO @ Fri, 26 Jun 2020 08:30:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:30:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:30:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:30:10: #1 total tags in treatment: 12209026 INFO @ Fri, 26 Jun 2020 08:30:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:30:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:30:10: #1 tags after filtering in treatment: 12209026 INFO @ Fri, 26 Jun 2020 08:30:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:30:10: #1 finished! INFO @ Fri, 26 Jun 2020 08:30:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:30:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:30:11: #2 number of paired peaks: 2137 INFO @ Fri, 26 Jun 2020 08:30:11: start model_add_line... INFO @ Fri, 26 Jun 2020 08:30:11: start X-correlation... INFO @ Fri, 26 Jun 2020 08:30:11: end of X-cor INFO @ Fri, 26 Jun 2020 08:30:11: #2 finished! INFO @ Fri, 26 Jun 2020 08:30:11: #2 predicted fragment length is 201 bps INFO @ Fri, 26 Jun 2020 08:30:11: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 26 Jun 2020 08:30:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.10_model.r INFO @ Fri, 26 Jun 2020 08:30:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:30:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:30:12: 7000000 INFO @ Fri, 26 Jun 2020 08:30:18: 8000000 INFO @ Fri, 26 Jun 2020 08:30:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:30:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:30:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.05_summits.bed INFO @ Fri, 26 Jun 2020 08:30:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8682 records, 4 fields): 11 millis INFO @ Fri, 26 Jun 2020 08:30:23: 9000000 CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:30:28: 10000000 INFO @ Fri, 26 Jun 2020 08:30:33: 11000000 INFO @ Fri, 26 Jun 2020 08:30:38: 12000000 INFO @ Fri, 26 Jun 2020 08:30:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:30:39: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:30:39: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:30:39: #1 total tags in treatment: 12209026 INFO @ Fri, 26 Jun 2020 08:30:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:30:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:30:40: #1 tags after filtering in treatment: 12209026 INFO @ Fri, 26 Jun 2020 08:30:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:30:40: #1 finished! INFO @ Fri, 26 Jun 2020 08:30:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:30:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:30:41: #2 number of paired peaks: 2137 INFO @ Fri, 26 Jun 2020 08:30:41: start model_add_line... INFO @ Fri, 26 Jun 2020 08:30:41: start X-correlation... INFO @ Fri, 26 Jun 2020 08:30:41: end of X-cor INFO @ Fri, 26 Jun 2020 08:30:41: #2 finished! INFO @ Fri, 26 Jun 2020 08:30:41: #2 predicted fragment length is 201 bps INFO @ Fri, 26 Jun 2020 08:30:41: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 26 Jun 2020 08:30:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.20_model.r INFO @ Fri, 26 Jun 2020 08:30:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:30:41: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:30:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:30:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:30:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.10_summits.bed INFO @ Fri, 26 Jun 2020 08:30:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5818 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:31:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:31:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:31:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:31:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467114/SRX467114.20_summits.bed INFO @ Fri, 26 Jun 2020 08:31:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2656 records, 4 fields): 5 millis CompletedMACS2peakCalling