Job ID = 6458991 SRX = SRX5850003 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:47:52 prefetch.2.10.7: 1) Downloading 'SRR9074480'... 2020-06-21T12:47:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:50:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:50:46 prefetch.2.10.7: 1) 'SRR9074480' was downloaded successfully 2020-06-21T12:50:46 prefetch.2.10.7: 'SRR9074480' has 0 unresolved dependencies Read 47372438 spots for SRR9074480/SRR9074480.sra Written 47372438 spots for SRR9074480/SRR9074480.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: 00:05:44 47372438 reads; of these: 47372438 (100.00%) were unpaired; of these: 39027544 (82.38%) aligned 0 times 7191473 (15.18%) aligned exactly 1 time 1153421 (2.43%) aligned >1 times 17.62% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 1178007 / 8344894 = 0.1412 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 22:00:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.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 22:00:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:54: 1000000 INFO @ Sun, 21 Jun 2020 22:00:59: 2000000 INFO @ Sun, 21 Jun 2020 22:01:05: 3000000 INFO @ Sun, 21 Jun 2020 22:01:10: 4000000 INFO @ Sun, 21 Jun 2020 22:01:15: 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 22:01:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.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 22:01:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:01:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:01:21: 6000000 INFO @ Sun, 21 Jun 2020 22:01:24: 1000000 INFO @ Sun, 21 Jun 2020 22:01:26: 7000000 INFO @ Sun, 21 Jun 2020 22:01:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:01:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:01:27: #1 total tags in treatment: 7166887 INFO @ Sun, 21 Jun 2020 22:01:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:27: #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 22:01:28: #1 tags after filtering in treatment: 7166592 INFO @ Sun, 21 Jun 2020 22:01:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:29: #2 number of paired peaks: 11311 INFO @ Sun, 21 Jun 2020 22:01:29: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:29: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:29: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:29: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:29: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 22:01:29: #2 alternative fragment length(s) may be 4,193 bps INFO @ Sun, 21 Jun 2020 22:01:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.05_model.r INFO @ Sun, 21 Jun 2020 22:01:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:01:30: 2000000 INFO @ Sun, 21 Jun 2020 22:01:35: 3000000 INFO @ Sun, 21 Jun 2020 22:01:40: 4000000 INFO @ Sun, 21 Jun 2020 22:01:45: 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 22:01:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.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 22:01:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:01:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:01:51: 6000000 INFO @ Sun, 21 Jun 2020 22:01:54: 1000000 INFO @ Sun, 21 Jun 2020 22:01:57: 7000000 INFO @ Sun, 21 Jun 2020 22:01:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:01:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:01:58: #1 total tags in treatment: 7166887 INFO @ Sun, 21 Jun 2020 22:01:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:58: #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 22:01:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.05_summits.bed INFO @ Sun, 21 Jun 2020 22:01:58: Done! INFO @ Sun, 21 Jun 2020 22:01:58: #1 tags after filtering in treatment: 7166592 INFO @ Sun, 21 Jun 2020 22:01:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:58: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:58: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (106 chroms): 2 millis pass2 - checking and writing primary data (7820 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:01:59: #2 number of paired peaks: 11311 INFO @ Sun, 21 Jun 2020 22:01:59: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:59: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:59: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:59: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:59: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 22:01:59: #2 alternative fragment length(s) may be 4,193 bps INFO @ Sun, 21 Jun 2020 22:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.10_model.r INFO @ Sun, 21 Jun 2020 22:01:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:00: 2000000 INFO @ Sun, 21 Jun 2020 22:02:05: 3000000 INFO @ Sun, 21 Jun 2020 22:02:11: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:02:16: 5000000 INFO @ Sun, 21 Jun 2020 22:02:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:21: 6000000 INFO @ Sun, 21 Jun 2020 22:02:27: 7000000 INFO @ Sun, 21 Jun 2020 22:02:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:02:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:02:28: #1 total tags in treatment: 7166887 INFO @ Sun, 21 Jun 2020 22:02:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:28: #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 22:02:28: #1 tags after filtering in treatment: 7166592 INFO @ Sun, 21 Jun 2020 22:02:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.10_summits.bed INFO @ Sun, 21 Jun 2020 22:02:29: Done! pass1 - making usageList (87 chroms): 3 millis pass2 - checking and writing primary data (3854 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:02:29: #2 number of paired peaks: 11311 INFO @ Sun, 21 Jun 2020 22:02:29: start model_add_line... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:02:29: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:29: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:29: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:29: #2 predicted fragment length is 193 bps INFO @ Sun, 21 Jun 2020 22:02:29: #2 alternative fragment length(s) may be 4,193 bps INFO @ Sun, 21 Jun 2020 22:02:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.20_model.r INFO @ Sun, 21 Jun 2020 22:02:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5850003/SRX5850003.20_summits.bed INFO @ Sun, 21 Jun 2020 22:02:58: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (1175 records, 4 fields): 5 millis CompletedMACS2peakCalling