Job ID = 6455339 SRX = SRX287708 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:40 prefetch.2.10.7: 1) Downloading 'SRR869896'... 2020-06-21T09:48:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:52:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:52:20 prefetch.2.10.7: 1) 'SRR869896' was downloaded successfully Read 19977921 spots for SRR869896/SRR869896.sra Written 19977921 spots for SRR869896/SRR869896.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: 00:04:38 19977921 reads; of these: 19977921 (100.00%) were unpaired; of these: 1786449 (8.94%) aligned 0 times 16746338 (83.82%) aligned exactly 1 time 1445134 (7.23%) aligned >1 times 91.06% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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] 2327221 / 18191472 = 0.1279 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 19:02:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.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 19:02:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:43: 1000000 INFO @ Sun, 21 Jun 2020 19:02:48: 2000000 INFO @ Sun, 21 Jun 2020 19:02:53: 3000000 INFO @ Sun, 21 Jun 2020 19:02:59: 4000000 INFO @ Sun, 21 Jun 2020 19:03:04: 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 19:03:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.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 19:03:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:09: 6000000 INFO @ Sun, 21 Jun 2020 19:03:13: 1000000 INFO @ Sun, 21 Jun 2020 19:03:15: 7000000 INFO @ Sun, 21 Jun 2020 19:03:19: 2000000 INFO @ Sun, 21 Jun 2020 19:03:21: 8000000 INFO @ Sun, 21 Jun 2020 19:03:25: 3000000 INFO @ Sun, 21 Jun 2020 19:03:27: 9000000 INFO @ Sun, 21 Jun 2020 19:03:31: 4000000 INFO @ Sun, 21 Jun 2020 19:03:33: 10000000 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 19:03:37: 5000000 INFO @ Sun, 21 Jun 2020 19:03:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.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 19:03:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:39: 11000000 INFO @ Sun, 21 Jun 2020 19:03:43: 6000000 INFO @ Sun, 21 Jun 2020 19:03:44: 1000000 INFO @ Sun, 21 Jun 2020 19:03:45: 12000000 INFO @ Sun, 21 Jun 2020 19:03:49: 7000000 INFO @ Sun, 21 Jun 2020 19:03:51: 13000000 INFO @ Sun, 21 Jun 2020 19:03:51: 2000000 INFO @ Sun, 21 Jun 2020 19:03:55: 8000000 INFO @ Sun, 21 Jun 2020 19:03:58: 14000000 INFO @ Sun, 21 Jun 2020 19:03:58: 3000000 INFO @ Sun, 21 Jun 2020 19:04:01: 9000000 INFO @ Sun, 21 Jun 2020 19:04:04: 15000000 INFO @ Sun, 21 Jun 2020 19:04:06: 4000000 INFO @ Sun, 21 Jun 2020 19:04:08: 10000000 INFO @ Sun, 21 Jun 2020 19:04:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:10: #1 total tags in treatment: 15864251 INFO @ Sun, 21 Jun 2020 19:04:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:10: #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 19:04:10: #1 tags after filtering in treatment: 15864231 INFO @ Sun, 21 Jun 2020 19:04:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:10: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:11: #2 number of paired peaks: 542 WARNING @ Sun, 21 Jun 2020 19:04:11: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:11: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:11: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 19:04:11: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 19:04:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.05_model.r INFO @ Sun, 21 Jun 2020 19:04:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:13: 5000000 INFO @ Sun, 21 Jun 2020 19:04:14: 11000000 INFO @ Sun, 21 Jun 2020 19:04:20: 6000000 INFO @ Sun, 21 Jun 2020 19:04:20: 12000000 INFO @ Sun, 21 Jun 2020 19:04:26: 13000000 INFO @ Sun, 21 Jun 2020 19:04:27: 7000000 INFO @ Sun, 21 Jun 2020 19:04:33: 14000000 INFO @ Sun, 21 Jun 2020 19:04:34: 8000000 INFO @ Sun, 21 Jun 2020 19:04:39: 15000000 INFO @ Sun, 21 Jun 2020 19:04:41: 9000000 INFO @ Sun, 21 Jun 2020 19:04:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:45: #1 total tags in treatment: 15864251 INFO @ Sun, 21 Jun 2020 19:04:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:45: #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 19:04:45: #1 tags after filtering in treatment: 15864231 INFO @ Sun, 21 Jun 2020 19:04:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:46: #2 number of paired peaks: 542 WARNING @ Sun, 21 Jun 2020 19:04:46: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:46: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 19:04:46: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 19:04:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.10_model.r INFO @ Sun, 21 Jun 2020 19:04:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:46: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:04:48: 10000000 INFO @ Sun, 21 Jun 2020 19:04:54: 11000000 INFO @ Sun, 21 Jun 2020 19:05:01: 12000000 INFO @ Sun, 21 Jun 2020 19:05:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.05_summits.bed INFO @ Sun, 21 Jun 2020 19:05:02: Done! pass1 - making usageList (126 chroms): 1 millis pass2 - checking and writing primary data (8006 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:07: 13000000 INFO @ Sun, 21 Jun 2020 19:05:14: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:05:20: 15000000 INFO @ Sun, 21 Jun 2020 19:05:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:05:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:05:26: #1 total tags in treatment: 15864251 INFO @ Sun, 21 Jun 2020 19:05:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:26: #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 19:05:26: #1 tags after filtering in treatment: 15864231 INFO @ Sun, 21 Jun 2020 19:05:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:28: #2 number of paired peaks: 542 WARNING @ Sun, 21 Jun 2020 19:05:28: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Sun, 21 Jun 2020 19:05:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:28: #2 predicted fragment length is 175 bps INFO @ Sun, 21 Jun 2020 19:05:28: #2 alternative fragment length(s) may be 175 bps INFO @ Sun, 21 Jun 2020 19:05:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.20_model.r INFO @ Sun, 21 Jun 2020 19:05:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.10_summits.bed INFO @ Sun, 21 Jun 2020 19:05:39: Done! pass1 - making usageList (84 chroms): 2 millis pass2 - checking and writing primary data (5517 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:06:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287708/SRX287708.20_summits.bed INFO @ Sun, 21 Jun 2020 19:06:17: Done! pass1 - making usageList (52 chroms): 2 millis pass2 - checking and writing primary data (3322 records, 4 fields): 6 millis CompletedMACS2peakCalling