Job ID = 6455705 SRX = SRX288005 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:13:36 prefetch.2.10.7: 1) Downloading 'SRR870194'... 2020-06-21T10:13:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:15:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:15:32 prefetch.2.10.7: 'SRR870194' is valid 2020-06-21T10:15:32 prefetch.2.10.7: 1) 'SRR870194' was downloaded successfully Read 13725225 spots for SRR870194/SRR870194.sra Written 13725225 spots for SRR870194/SRR870194.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: 00:03:21 13725225 reads; of these: 13725225 (100.00%) were unpaired; of these: 1110428 (8.09%) aligned 0 times 10508408 (76.56%) aligned exactly 1 time 2106389 (15.35%) aligned >1 times 91.91% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 2258158 / 12614797 = 0.1790 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 19:23:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.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 19:23:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:15: 1000000 INFO @ Sun, 21 Jun 2020 19:23:20: 2000000 INFO @ Sun, 21 Jun 2020 19:23:25: 3000000 INFO @ Sun, 21 Jun 2020 19:23:30: 4000000 INFO @ Sun, 21 Jun 2020 19:23:35: 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 19:23:40: 6000000 INFO @ Sun, 21 Jun 2020 19:23:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.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 19:23:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:45: 7000000 INFO @ Sun, 21 Jun 2020 19:23:45: 1000000 INFO @ Sun, 21 Jun 2020 19:23:50: 8000000 INFO @ Sun, 21 Jun 2020 19:23:51: 2000000 INFO @ Sun, 21 Jun 2020 19:23:56: 3000000 INFO @ Sun, 21 Jun 2020 19:23:56: 9000000 INFO @ Sun, 21 Jun 2020 19:24:01: 4000000 INFO @ Sun, 21 Jun 2020 19:24:02: 10000000 INFO @ Sun, 21 Jun 2020 19:24:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:04: #1 total tags in treatment: 10356639 INFO @ Sun, 21 Jun 2020 19:24:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:04: #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 19:24:05: #1 tags after filtering in treatment: 10356636 INFO @ Sun, 21 Jun 2020 19:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:05: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:06: #2 number of paired peaks: 4796 INFO @ Sun, 21 Jun 2020 19:24:06: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:06: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:06: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:06: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:06: #2 predicted fragment length is 249 bps INFO @ Sun, 21 Jun 2020 19:24:06: #2 alternative fragment length(s) may be 249 bps INFO @ Sun, 21 Jun 2020 19:24:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.05_model.r INFO @ Sun, 21 Jun 2020 19:24:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:06: 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 @ Sun, 21 Jun 2020 19:24:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.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 19:24:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:12: 6000000 INFO @ Sun, 21 Jun 2020 19:24:16: 1000000 INFO @ Sun, 21 Jun 2020 19:24:17: 7000000 INFO @ Sun, 21 Jun 2020 19:24:22: 8000000 INFO @ Sun, 21 Jun 2020 19:24:22: 2000000 INFO @ Sun, 21 Jun 2020 19:24:28: 9000000 INFO @ Sun, 21 Jun 2020 19:24:28: 3000000 INFO @ Sun, 21 Jun 2020 19:24:33: 10000000 INFO @ Sun, 21 Jun 2020 19:24:34: 4000000 INFO @ Sun, 21 Jun 2020 19:24:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:36: #1 total tags in treatment: 10356639 INFO @ Sun, 21 Jun 2020 19:24:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:36: #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 19:24:36: #1 tags after filtering in treatment: 10356636 INFO @ Sun, 21 Jun 2020 19:24:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:37: #2 number of paired peaks: 4796 INFO @ Sun, 21 Jun 2020 19:24:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:37: #2 predicted fragment length is 249 bps INFO @ Sun, 21 Jun 2020 19:24:37: #2 alternative fragment length(s) may be 249 bps INFO @ Sun, 21 Jun 2020 19:24:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.10_model.r INFO @ Sun, 21 Jun 2020 19:24:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:40: 5000000 INFO @ Sun, 21 Jun 2020 19:24:46: 6000000 INFO @ Sun, 21 Jun 2020 19:24:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.05_summits.bed INFO @ Sun, 21 Jun 2020 19:24:51: Done! pass1 - making usageList (480 chroms): 2 millis pass2 - checking and writing primary data (8758 records, 4 fields): 21 millis INFO @ Sun, 21 Jun 2020 19:24:51: 7000000 CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:24:57: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:25:03: 9000000 INFO @ Sun, 21 Jun 2020 19:25:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:09: 10000000 INFO @ Sun, 21 Jun 2020 19:25:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:12: #1 total tags in treatment: 10356639 INFO @ Sun, 21 Jun 2020 19:25:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:12: #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 19:25:12: #1 tags after filtering in treatment: 10356636 INFO @ Sun, 21 Jun 2020 19:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:13: #2 number of paired peaks: 4796 INFO @ Sun, 21 Jun 2020 19:25:13: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:13: #2 predicted fragment length is 249 bps INFO @ Sun, 21 Jun 2020 19:25:13: #2 alternative fragment length(s) may be 249 bps INFO @ Sun, 21 Jun 2020 19:25:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.20_model.r INFO @ Sun, 21 Jun 2020 19:25:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:25:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.10_summits.bed INFO @ Sun, 21 Jun 2020 19:25:21: Done! pass1 - making usageList (347 chroms): 2 millis pass2 - checking and writing primary data (7016 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:25:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288005/SRX288005.20_summits.bed INFO @ Sun, 21 Jun 2020 19:25:58: Done! pass1 - making usageList (165 chroms): 1 millis pass2 - checking and writing primary data (5152 records, 4 fields): 11 millis CompletedMACS2peakCalling