Job ID = 6459890 SRX = SRX969922 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:47:34 prefetch.2.10.7: 1) Downloading 'SRR1931638'... 2020-06-21T13:47:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:49:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:49:16 prefetch.2.10.7: 'SRR1931638' is valid 2020-06-21T13:49:16 prefetch.2.10.7: 1) 'SRR1931638' was downloaded successfully Read 15324494 spots for SRR1931638/SRR1931638.sra Written 15324494 spots for SRR1931638/SRR1931638.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: 00:04:41 15324494 reads; of these: 15324494 (100.00%) were unpaired; of these: 874789 (5.71%) aligned 0 times 10859411 (70.86%) aligned exactly 1 time 3590294 (23.43%) aligned >1 times 94.29% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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] 3238486 / 14449705 = 0.2241 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 22:57:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.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 22:57:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:57:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:58:06: 1000000 INFO @ Sun, 21 Jun 2020 22:58:13: 2000000 INFO @ Sun, 21 Jun 2020 22:58:20: 3000000 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 22:58:28: 4000000 INFO @ Sun, 21 Jun 2020 22:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.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 22:58:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:58:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:58:35: 5000000 INFO @ Sun, 21 Jun 2020 22:58:36: 1000000 INFO @ Sun, 21 Jun 2020 22:58:43: 6000000 INFO @ Sun, 21 Jun 2020 22:58:44: 2000000 INFO @ Sun, 21 Jun 2020 22:58:50: 7000000 INFO @ Sun, 21 Jun 2020 22:58:51: 3000000 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 22:58:58: 8000000 INFO @ Sun, 21 Jun 2020 22:58:59: 4000000 INFO @ Sun, 21 Jun 2020 22:58:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.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 22:58:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:58:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:59:06: 9000000 INFO @ Sun, 21 Jun 2020 22:59:06: 5000000 INFO @ Sun, 21 Jun 2020 22:59:07: 1000000 INFO @ Sun, 21 Jun 2020 22:59:14: 6000000 INFO @ Sun, 21 Jun 2020 22:59:14: 10000000 INFO @ Sun, 21 Jun 2020 22:59:15: 2000000 INFO @ Sun, 21 Jun 2020 22:59:21: 7000000 INFO @ Sun, 21 Jun 2020 22:59:23: 11000000 INFO @ Sun, 21 Jun 2020 22:59:24: 3000000 INFO @ Sun, 21 Jun 2020 22:59:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:59:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:59:24: #1 total tags in treatment: 11211219 INFO @ Sun, 21 Jun 2020 22:59:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:24: #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 22:59:25: #1 tags after filtering in treatment: 11211214 INFO @ Sun, 21 Jun 2020 22:59:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:25: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:26: #2 number of paired peaks: 2895 INFO @ Sun, 21 Jun 2020 22:59:26: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:26: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:26: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:26: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:26: #2 predicted fragment length is 217 bps INFO @ Sun, 21 Jun 2020 22:59:26: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 21 Jun 2020 22:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.05_model.r INFO @ Sun, 21 Jun 2020 22:59:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:59:29: 8000000 INFO @ Sun, 21 Jun 2020 22:59:32: 4000000 INFO @ Sun, 21 Jun 2020 22:59:36: 9000000 INFO @ Sun, 21 Jun 2020 22:59:40: 5000000 INFO @ Sun, 21 Jun 2020 22:59:44: 10000000 INFO @ Sun, 21 Jun 2020 22:59:48: 6000000 INFO @ Sun, 21 Jun 2020 22:59:52: 11000000 INFO @ Sun, 21 Jun 2020 22:59:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:59:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:59:53: #1 total tags in treatment: 11211219 INFO @ Sun, 21 Jun 2020 22:59:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:53: #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 22:59:54: #1 tags after filtering in treatment: 11211214 INFO @ Sun, 21 Jun 2020 22:59:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:54: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:55: #2 number of paired peaks: 2895 INFO @ Sun, 21 Jun 2020 22:59:55: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:55: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:55: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:55: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:55: #2 predicted fragment length is 217 bps INFO @ Sun, 21 Jun 2020 22:59:55: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 21 Jun 2020 22:59:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.10_model.r INFO @ Sun, 21 Jun 2020 22:59:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:59:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:59:55: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:00:02: 8000000 INFO @ Sun, 21 Jun 2020 23:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.05_summits.bed INFO @ Sun, 21 Jun 2020 23:00:08: Done! pass1 - making usageList (540 chroms): 1 millis pass2 - checking and writing primary data (6841 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:00:10: 9000000 INFO @ Sun, 21 Jun 2020 23:00:17: 10000000 INFO @ Sun, 21 Jun 2020 23:00:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:00:24: 11000000 INFO @ Sun, 21 Jun 2020 23:00:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:00:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:00:26: #1 total tags in treatment: 11211219 INFO @ Sun, 21 Jun 2020 23:00:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:00:26: #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 23:00:26: #1 tags after filtering in treatment: 11211214 INFO @ Sun, 21 Jun 2020 23:00:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:00:26: #1 finished! INFO @ Sun, 21 Jun 2020 23:00:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:00:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:00:27: #2 number of paired peaks: 2895 INFO @ Sun, 21 Jun 2020 23:00:27: start model_add_line... INFO @ Sun, 21 Jun 2020 23:00:27: start X-correlation... INFO @ Sun, 21 Jun 2020 23:00:27: end of X-cor INFO @ Sun, 21 Jun 2020 23:00:27: #2 finished! INFO @ Sun, 21 Jun 2020 23:00:27: #2 predicted fragment length is 217 bps INFO @ Sun, 21 Jun 2020 23:00:27: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 21 Jun 2020 23:00:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.20_model.r INFO @ Sun, 21 Jun 2020 23:00:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:00:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:00:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:00:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:00:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.10_summits.bed INFO @ Sun, 21 Jun 2020 23:00:35: Done! pass1 - making usageList (428 chroms): 1 millis pass2 - checking and writing primary data (5719 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:00:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969922/SRX969922.20_summits.bed INFO @ Sun, 21 Jun 2020 23:01:08: Done! pass1 - making usageList (328 chroms): 1 millis pass2 - checking and writing primary data (4526 records, 4 fields): 15 millis CompletedMACS2peakCalling