Job ID = 6452821 SRX = SRX041381 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:49:45 prefetch.2.10.7: 1) Downloading 'SRR099108'... 2020-06-21T07:49:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:53:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:53:46 prefetch.2.10.7: 'SRR099108' is valid 2020-06-21T07:53:46 prefetch.2.10.7: 1) 'SRR099108' was downloaded successfully Read 24847144 spots for SRR099108/SRR099108.sra Written 24847144 spots for SRR099108/SRR099108.sra 2020-06-21T07:54:59 prefetch.2.10.7: 1) Downloading 'SRR099109'... 2020-06-21T07:54:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:58:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:58:25 prefetch.2.10.7: 1) 'SRR099109' was downloaded successfully Read 28483105 spots for SRR099109/SRR099109.sra Written 28483105 spots for SRR099109/SRR099109.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: 00:08:58 53330249 reads; of these: 53330249 (100.00%) were unpaired; of these: 3373014 (6.32%) aligned 0 times 43802373 (82.13%) aligned exactly 1 time 6154862 (11.54%) aligned >1 times 93.68% overall alignment rate Time searching: 00:08:58 Overall time: 00:08:58 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 16 files... [bam_rmdupse_core] 23664475 / 49957235 = 0.4737 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 17:16:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.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 17:16:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:16:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:16:32: 1000000 INFO @ Sun, 21 Jun 2020 17:16:38: 2000000 INFO @ Sun, 21 Jun 2020 17:16:44: 3000000 INFO @ Sun, 21 Jun 2020 17:16:50: 4000000 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 17:16:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.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 17:16:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:16:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:16:57: 5000000 INFO @ Sun, 21 Jun 2020 17:17:02: 1000000 INFO @ Sun, 21 Jun 2020 17:17:04: 6000000 INFO @ Sun, 21 Jun 2020 17:17:09: 2000000 INFO @ Sun, 21 Jun 2020 17:17:10: 7000000 INFO @ Sun, 21 Jun 2020 17:17:16: 3000000 INFO @ Sun, 21 Jun 2020 17:17:17: 8000000 INFO @ Sun, 21 Jun 2020 17:17:23: 4000000 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 17:17:24: 9000000 INFO @ Sun, 21 Jun 2020 17:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.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 17:17:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:17:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:17:30: 5000000 INFO @ Sun, 21 Jun 2020 17:17:31: 10000000 INFO @ Sun, 21 Jun 2020 17:17:32: 1000000 INFO @ Sun, 21 Jun 2020 17:17:37: 6000000 INFO @ Sun, 21 Jun 2020 17:17:38: 11000000 INFO @ Sun, 21 Jun 2020 17:17:38: 2000000 INFO @ Sun, 21 Jun 2020 17:17:44: 7000000 INFO @ Sun, 21 Jun 2020 17:17:44: 12000000 INFO @ Sun, 21 Jun 2020 17:17:45: 3000000 INFO @ Sun, 21 Jun 2020 17:17:51: 8000000 INFO @ Sun, 21 Jun 2020 17:17:51: 4000000 INFO @ Sun, 21 Jun 2020 17:17:51: 13000000 INFO @ Sun, 21 Jun 2020 17:17:57: 5000000 INFO @ Sun, 21 Jun 2020 17:17:58: 9000000 INFO @ Sun, 21 Jun 2020 17:17:58: 14000000 INFO @ Sun, 21 Jun 2020 17:18:04: 6000000 INFO @ Sun, 21 Jun 2020 17:18:05: 10000000 INFO @ Sun, 21 Jun 2020 17:18:05: 15000000 INFO @ Sun, 21 Jun 2020 17:18:10: 7000000 INFO @ Sun, 21 Jun 2020 17:18:12: 11000000 INFO @ Sun, 21 Jun 2020 17:18:12: 16000000 INFO @ Sun, 21 Jun 2020 17:18:17: 8000000 INFO @ Sun, 21 Jun 2020 17:18:18: 12000000 INFO @ Sun, 21 Jun 2020 17:18:19: 17000000 INFO @ Sun, 21 Jun 2020 17:18:23: 9000000 INFO @ Sun, 21 Jun 2020 17:18:25: 13000000 INFO @ Sun, 21 Jun 2020 17:18:25: 18000000 INFO @ Sun, 21 Jun 2020 17:18:29: 10000000 INFO @ Sun, 21 Jun 2020 17:18:32: 19000000 INFO @ Sun, 21 Jun 2020 17:18:32: 14000000 INFO @ Sun, 21 Jun 2020 17:18:36: 11000000 INFO @ Sun, 21 Jun 2020 17:18:39: 20000000 INFO @ Sun, 21 Jun 2020 17:18:39: 15000000 INFO @ Sun, 21 Jun 2020 17:18:42: 12000000 INFO @ Sun, 21 Jun 2020 17:18:46: 16000000 INFO @ Sun, 21 Jun 2020 17:18:46: 21000000 INFO @ Sun, 21 Jun 2020 17:18:48: 13000000 INFO @ Sun, 21 Jun 2020 17:18:53: 22000000 INFO @ Sun, 21 Jun 2020 17:18:53: 17000000 INFO @ Sun, 21 Jun 2020 17:18:54: 14000000 INFO @ Sun, 21 Jun 2020 17:19:00: 23000000 INFO @ Sun, 21 Jun 2020 17:19:00: 18000000 INFO @ Sun, 21 Jun 2020 17:19:01: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:19:07: 24000000 INFO @ Sun, 21 Jun 2020 17:19:07: 16000000 INFO @ Sun, 21 Jun 2020 17:19:07: 19000000 INFO @ Sun, 21 Jun 2020 17:19:13: 17000000 INFO @ Sun, 21 Jun 2020 17:19:14: 25000000 INFO @ Sun, 21 Jun 2020 17:19:14: 20000000 INFO @ Sun, 21 Jun 2020 17:19:19: 18000000 INFO @ Sun, 21 Jun 2020 17:19:21: 26000000 INFO @ Sun, 21 Jun 2020 17:19:21: 21000000 INFO @ Sun, 21 Jun 2020 17:19:23: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:19:23: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:19:23: #1 total tags in treatment: 26292760 INFO @ Sun, 21 Jun 2020 17:19:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:19:23: #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 17:19:23: #1 tags after filtering in treatment: 26292735 INFO @ Sun, 21 Jun 2020 17:19:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:19:23: #1 finished! INFO @ Sun, 21 Jun 2020 17:19:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:19:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:19:25: #2 number of paired peaks: 139 WARNING @ Sun, 21 Jun 2020 17:19:25: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sun, 21 Jun 2020 17:19:25: start model_add_line... INFO @ Sun, 21 Jun 2020 17:19:25: start X-correlation... INFO @ Sun, 21 Jun 2020 17:19:25: end of X-cor INFO @ Sun, 21 Jun 2020 17:19:25: #2 finished! INFO @ Sun, 21 Jun 2020 17:19:25: #2 predicted fragment length is 181 bps INFO @ Sun, 21 Jun 2020 17:19:25: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 21 Jun 2020 17:19:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.05_model.r INFO @ Sun, 21 Jun 2020 17:19:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:19:25: 19000000 INFO @ Sun, 21 Jun 2020 17:19:28: 22000000 INFO @ Sun, 21 Jun 2020 17:19:32: 20000000 INFO @ Sun, 21 Jun 2020 17:19:35: 23000000 INFO @ Sun, 21 Jun 2020 17:19:38: 21000000 INFO @ Sun, 21 Jun 2020 17:19:42: 24000000 INFO @ Sun, 21 Jun 2020 17:19:44: 22000000 INFO @ Sun, 21 Jun 2020 17:19:49: 25000000 INFO @ Sun, 21 Jun 2020 17:19:50: 23000000 INFO @ Sun, 21 Jun 2020 17:19:56: 26000000 INFO @ Sun, 21 Jun 2020 17:19:57: 24000000 INFO @ Sun, 21 Jun 2020 17:19:58: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:19:58: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:19:58: #1 total tags in treatment: 26292760 INFO @ Sun, 21 Jun 2020 17:19:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:19:58: #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 17:19:59: #1 tags after filtering in treatment: 26292735 INFO @ Sun, 21 Jun 2020 17:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:19:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:19:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:20:00: #2 number of paired peaks: 139 WARNING @ Sun, 21 Jun 2020 17:20:00: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sun, 21 Jun 2020 17:20:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:00: #2 predicted fragment length is 181 bps INFO @ Sun, 21 Jun 2020 17:20:00: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 21 Jun 2020 17:20:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.10_model.r INFO @ Sun, 21 Jun 2020 17:20:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:20:02: 25000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:20:08: 26000000 INFO @ Sun, 21 Jun 2020 17:20:10: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:20:10: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:20:10: #1 total tags in treatment: 26292760 INFO @ Sun, 21 Jun 2020 17:20:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:20:10: #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 17:20:10: #1 tags after filtering in treatment: 26292735 INFO @ Sun, 21 Jun 2020 17:20:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:20:10: #1 finished! INFO @ Sun, 21 Jun 2020 17:20:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:20:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:20:12: #2 number of paired peaks: 139 WARNING @ Sun, 21 Jun 2020 17:20:12: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sun, 21 Jun 2020 17:20:12: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:12: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:12: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:12: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:12: #2 predicted fragment length is 181 bps INFO @ Sun, 21 Jun 2020 17:20:12: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 21 Jun 2020 17:20:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.20_model.r INFO @ Sun, 21 Jun 2020 17:20:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:20:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:20:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:20:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:20:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.05_summits.bed INFO @ Sun, 21 Jun 2020 17:20:43: Done! pass1 - making usageList (498 chroms): 2 millis pass2 - checking and writing primary data (6449 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:20:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.10_summits.bed INFO @ Sun, 21 Jun 2020 17:21:17: Done! pass1 - making usageList (411 chroms): 2 millis pass2 - checking and writing primary data (2897 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:21:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041381/SRX041381.20_summits.bed INFO @ Sun, 21 Jun 2020 17:21:26: Done! pass1 - making usageList (216 chroms): 1 millis pass2 - checking and writing primary data (1023 records, 4 fields): 7 millis CompletedMACS2peakCalling