Job ID = 6452895 SRX = SRX041396 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:46:00 prefetch.2.10.7: 1) Downloading 'SRR099130'... 2020-06-21T07:46:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:51:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:51:27 prefetch.2.10.7: 'SRR099130' is valid 2020-06-21T07:51:27 prefetch.2.10.7: 1) 'SRR099130' was downloaded successfully Read 19706651 spots for SRR099130/SRR099130.sra Written 19706651 spots for SRR099130/SRR099130.sra 2020-06-21T07:52:28 prefetch.2.10.7: 1) Downloading 'SRR099131'... 2020-06-21T07:52:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:56:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:56:51 prefetch.2.10.7: 'SRR099131' is valid 2020-06-21T07:56:51 prefetch.2.10.7: 1) 'SRR099131' was downloaded successfully Read 19932071 spots for SRR099131/SRR099131.sra Written 19932071 spots for SRR099131/SRR099131.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: 00:08:57 39638722 reads; of these: 39638722 (100.00%) were unpaired; of these: 1250010 (3.15%) aligned 0 times 28727869 (72.47%) aligned exactly 1 time 9660843 (24.37%) aligned >1 times 96.85% overall alignment rate Time searching: 00:08:57 Overall time: 00:08:57 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 12 files... [bam_rmdupse_core] 14893685 / 38388712 = 0.3880 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 17:13:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.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 17:13:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:13:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:14:04: 1000000 INFO @ Sun, 21 Jun 2020 17:14:08: 2000000 INFO @ Sun, 21 Jun 2020 17:14:12: 3000000 INFO @ Sun, 21 Jun 2020 17:14:17: 4000000 INFO @ Sun, 21 Jun 2020 17:14:21: 5000000 INFO @ Sun, 21 Jun 2020 17:14:25: 6000000 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 17:14:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.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 17:14:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:14:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:14:30: 7000000 INFO @ Sun, 21 Jun 2020 17:14:34: 1000000 INFO @ Sun, 21 Jun 2020 17:14:34: 8000000 INFO @ Sun, 21 Jun 2020 17:14:38: 2000000 INFO @ Sun, 21 Jun 2020 17:14:38: 9000000 INFO @ Sun, 21 Jun 2020 17:14:43: 10000000 INFO @ Sun, 21 Jun 2020 17:14:43: 3000000 INFO @ Sun, 21 Jun 2020 17:14:47: 11000000 INFO @ Sun, 21 Jun 2020 17:14:47: 4000000 INFO @ Sun, 21 Jun 2020 17:14:51: 12000000 INFO @ Sun, 21 Jun 2020 17:14:51: 5000000 INFO @ Sun, 21 Jun 2020 17:14:55: 13000000 INFO @ Sun, 21 Jun 2020 17:14:56: 6000000 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 17:14:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.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 17:14:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:14:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:15:00: 14000000 INFO @ Sun, 21 Jun 2020 17:15:00: 7000000 INFO @ Sun, 21 Jun 2020 17:15:04: 1000000 INFO @ Sun, 21 Jun 2020 17:15:04: 15000000 INFO @ Sun, 21 Jun 2020 17:15:04: 8000000 INFO @ Sun, 21 Jun 2020 17:15:08: 16000000 INFO @ Sun, 21 Jun 2020 17:15:08: 2000000 INFO @ Sun, 21 Jun 2020 17:15:09: 9000000 INFO @ Sun, 21 Jun 2020 17:15:12: 17000000 INFO @ Sun, 21 Jun 2020 17:15:13: 3000000 INFO @ Sun, 21 Jun 2020 17:15:13: 10000000 INFO @ Sun, 21 Jun 2020 17:15:17: 18000000 INFO @ Sun, 21 Jun 2020 17:15:17: 4000000 INFO @ Sun, 21 Jun 2020 17:15:17: 11000000 INFO @ Sun, 21 Jun 2020 17:15:21: 19000000 INFO @ Sun, 21 Jun 2020 17:15:21: 5000000 INFO @ Sun, 21 Jun 2020 17:15:22: 12000000 INFO @ Sun, 21 Jun 2020 17:15:26: 20000000 INFO @ Sun, 21 Jun 2020 17:15:26: 6000000 INFO @ Sun, 21 Jun 2020 17:15:26: 13000000 INFO @ Sun, 21 Jun 2020 17:15:30: 21000000 INFO @ Sun, 21 Jun 2020 17:15:30: 7000000 INFO @ Sun, 21 Jun 2020 17:15:30: 14000000 INFO @ Sun, 21 Jun 2020 17:15:34: 22000000 INFO @ Sun, 21 Jun 2020 17:15:34: 8000000 INFO @ Sun, 21 Jun 2020 17:15:35: 15000000 INFO @ Sun, 21 Jun 2020 17:15:39: 23000000 INFO @ Sun, 21 Jun 2020 17:15:39: 9000000 INFO @ Sun, 21 Jun 2020 17:15:39: 16000000 INFO @ Sun, 21 Jun 2020 17:15:41: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:15:41: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:15:41: #1 total tags in treatment: 23495027 INFO @ Sun, 21 Jun 2020 17:15:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:15:41: #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 17:15:42: #1 tags after filtering in treatment: 23495012 INFO @ Sun, 21 Jun 2020 17:15:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:15:42: #1 finished! INFO @ Sun, 21 Jun 2020 17:15:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:15:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:15:43: 10000000 INFO @ Sun, 21 Jun 2020 17:15:43: 17000000 INFO @ Sun, 21 Jun 2020 17:15:43: #2 number of paired peaks: 983 WARNING @ Sun, 21 Jun 2020 17:15:43: Fewer paired peaks (983) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 983 pairs to build model! INFO @ Sun, 21 Jun 2020 17:15:43: start model_add_line... INFO @ Sun, 21 Jun 2020 17:15:43: start X-correlation... INFO @ Sun, 21 Jun 2020 17:15:43: end of X-cor INFO @ Sun, 21 Jun 2020 17:15:43: #2 finished! INFO @ Sun, 21 Jun 2020 17:15:43: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 17:15:43: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 17:15:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.05_model.r INFO @ Sun, 21 Jun 2020 17:15:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:15:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:15:47: 18000000 INFO @ Sun, 21 Jun 2020 17:15:47: 11000000 INFO @ Sun, 21 Jun 2020 17:15:52: 12000000 INFO @ Sun, 21 Jun 2020 17:15:52: 19000000 INFO @ Sun, 21 Jun 2020 17:15:56: 13000000 INFO @ Sun, 21 Jun 2020 17:15:56: 20000000 INFO @ Sun, 21 Jun 2020 17:16:00: 14000000 INFO @ Sun, 21 Jun 2020 17:16:01: 21000000 INFO @ Sun, 21 Jun 2020 17:16:05: 15000000 INFO @ Sun, 21 Jun 2020 17:16:05: 22000000 INFO @ Sun, 21 Jun 2020 17:16:09: 16000000 INFO @ Sun, 21 Jun 2020 17:16:09: 23000000 INFO @ Sun, 21 Jun 2020 17:16:12: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:16:12: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:16:12: #1 total tags in treatment: 23495027 INFO @ Sun, 21 Jun 2020 17:16:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:16:12: #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 17:16:12: #1 tags after filtering in treatment: 23495012 INFO @ Sun, 21 Jun 2020 17:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:16:12: #1 finished! INFO @ Sun, 21 Jun 2020 17:16:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:16:13: 17000000 INFO @ Sun, 21 Jun 2020 17:16:14: #2 number of paired peaks: 983 WARNING @ Sun, 21 Jun 2020 17:16:14: Fewer paired peaks (983) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 983 pairs to build model! INFO @ Sun, 21 Jun 2020 17:16:14: start model_add_line... INFO @ Sun, 21 Jun 2020 17:16:14: start X-correlation... INFO @ Sun, 21 Jun 2020 17:16:14: end of X-cor INFO @ Sun, 21 Jun 2020 17:16:14: #2 finished! INFO @ Sun, 21 Jun 2020 17:16:14: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 17:16:14: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 17:16:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.10_model.r INFO @ Sun, 21 Jun 2020 17:16:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:16:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:16:17: 18000000 INFO @ Sun, 21 Jun 2020 17:16:22: 19000000 INFO @ Sun, 21 Jun 2020 17:16:26: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:16:31: 21000000 INFO @ Sun, 21 Jun 2020 17:16:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:16:35: 22000000 INFO @ Sun, 21 Jun 2020 17:16:39: 23000000 INFO @ Sun, 21 Jun 2020 17:16:42: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:16:42: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:16:42: #1 total tags in treatment: 23495027 INFO @ Sun, 21 Jun 2020 17:16:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:16:42: #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 17:16:42: #1 tags after filtering in treatment: 23495012 INFO @ Sun, 21 Jun 2020 17:16:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:16:42: #1 finished! INFO @ Sun, 21 Jun 2020 17:16:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:16:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:16:44: #2 number of paired peaks: 983 WARNING @ Sun, 21 Jun 2020 17:16:44: Fewer paired peaks (983) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 983 pairs to build model! INFO @ Sun, 21 Jun 2020 17:16:44: start model_add_line... INFO @ Sun, 21 Jun 2020 17:16:44: start X-correlation... INFO @ Sun, 21 Jun 2020 17:16:44: end of X-cor INFO @ Sun, 21 Jun 2020 17:16:44: #2 finished! INFO @ Sun, 21 Jun 2020 17:16:44: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 17:16:44: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 17:16:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.20_model.r INFO @ Sun, 21 Jun 2020 17:16:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:16:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:16:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:16:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.05_summits.bed INFO @ Sun, 21 Jun 2020 17:16:56: Done! pass1 - making usageList (810 chroms): 5 millis pass2 - checking and writing primary data (32574 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:17:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:17:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:17:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:17:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.10_summits.bed INFO @ Sun, 21 Jun 2020 17:17:28: Done! pass1 - making usageList (692 chroms): 4 millis pass2 - checking and writing primary data (20705 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:17:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:17:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:17:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:17:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041396/SRX041396.20_summits.bed INFO @ Sun, 21 Jun 2020 17:17:55: Done! pass1 - making usageList (580 chroms): 2 millis pass2 - checking and writing primary data (8928 records, 4 fields): 22 millis CompletedMACS2peakCalling