Job ID = 6452651 SRX = SRX025462 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:42:52 prefetch.2.10.7: 1) Downloading 'SRR063854'... 2020-06-21T07:42:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:44:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:44:16 prefetch.2.10.7: 'SRR063854' is valid 2020-06-21T07:44:16 prefetch.2.10.7: 1) 'SRR063854' was downloaded successfully Read 9106740 spots for SRR063854/SRR063854.sra Written 9106740 spots for SRR063854/SRR063854.sra 2020-06-21T07:44:51 prefetch.2.10.7: 1) Downloading 'SRR063855'... 2020-06-21T07:44:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:47:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:47:56 prefetch.2.10.7: 'SRR063855' is valid 2020-06-21T07:47:56 prefetch.2.10.7: 1) 'SRR063855' was downloaded successfully Read 8771375 spots for SRR063855/SRR063855.sra Written 8771375 spots for SRR063855/SRR063855.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: 00:03:52 17878115 reads; of these: 17878115 (100.00%) were unpaired; of these: 586056 (3.28%) aligned 0 times 14081714 (78.77%) aligned exactly 1 time 3210345 (17.96%) aligned >1 times 96.72% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 3909976 / 17292059 = 0.2261 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 16:56:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.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 16:56:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:56:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:56:37: 1000000 INFO @ Sun, 21 Jun 2020 16:56:42: 2000000 INFO @ Sun, 21 Jun 2020 16:56:47: 3000000 INFO @ Sun, 21 Jun 2020 16:56:52: 4000000 INFO @ Sun, 21 Jun 2020 16:56:57: 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 16:57:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.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 16:57:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:57:02: 6000000 INFO @ Sun, 21 Jun 2020 16:57:07: 7000000 INFO @ Sun, 21 Jun 2020 16:57:08: 1000000 INFO @ Sun, 21 Jun 2020 16:57:13: 8000000 INFO @ Sun, 21 Jun 2020 16:57:14: 2000000 INFO @ Sun, 21 Jun 2020 16:57:19: 9000000 INFO @ Sun, 21 Jun 2020 16:57:21: 3000000 INFO @ Sun, 21 Jun 2020 16:57:25: 10000000 INFO @ Sun, 21 Jun 2020 16:57:27: 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 16:57:31: 11000000 INFO @ Sun, 21 Jun 2020 16:57:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.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 16:57:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:57:34: 5000000 INFO @ Sun, 21 Jun 2020 16:57:37: 12000000 INFO @ Sun, 21 Jun 2020 16:57:38: 1000000 INFO @ Sun, 21 Jun 2020 16:57:40: 6000000 INFO @ Sun, 21 Jun 2020 16:57:44: 13000000 INFO @ Sun, 21 Jun 2020 16:57:45: 2000000 INFO @ Sun, 21 Jun 2020 16:57:46: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:57:46: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:57:46: #1 total tags in treatment: 13382083 INFO @ Sun, 21 Jun 2020 16:57:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:57:46: #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 16:57:47: #1 tags after filtering in treatment: 13382057 INFO @ Sun, 21 Jun 2020 16:57:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:57:47: #1 finished! INFO @ Sun, 21 Jun 2020 16:57:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:57:47: 7000000 INFO @ Sun, 21 Jun 2020 16:57:47: #2 number of paired peaks: 587 WARNING @ Sun, 21 Jun 2020 16:57:47: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Sun, 21 Jun 2020 16:57:47: start model_add_line... INFO @ Sun, 21 Jun 2020 16:57:48: start X-correlation... INFO @ Sun, 21 Jun 2020 16:57:48: end of X-cor INFO @ Sun, 21 Jun 2020 16:57:48: #2 finished! INFO @ Sun, 21 Jun 2020 16:57:48: #2 predicted fragment length is 340 bps INFO @ Sun, 21 Jun 2020 16:57:48: #2 alternative fragment length(s) may be 340 bps INFO @ Sun, 21 Jun 2020 16:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.05_model.r INFO @ Sun, 21 Jun 2020 16:57:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:57:51: 3000000 INFO @ Sun, 21 Jun 2020 16:57:53: 8000000 INFO @ Sun, 21 Jun 2020 16:57:58: 4000000 INFO @ Sun, 21 Jun 2020 16:57:59: 9000000 INFO @ Sun, 21 Jun 2020 16:58:04: 5000000 INFO @ Sun, 21 Jun 2020 16:58:06: 10000000 INFO @ Sun, 21 Jun 2020 16:58:10: 6000000 INFO @ Sun, 21 Jun 2020 16:58:12: 11000000 INFO @ Sun, 21 Jun 2020 16:58:17: 7000000 INFO @ Sun, 21 Jun 2020 16:58:19: 12000000 INFO @ Sun, 21 Jun 2020 16:58:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:23: 8000000 INFO @ Sun, 21 Jun 2020 16:58:25: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:58:28: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:58:28: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:58:28: #1 total tags in treatment: 13382083 INFO @ Sun, 21 Jun 2020 16:58:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:28: #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 16:58:28: #1 tags after filtering in treatment: 13382057 INFO @ Sun, 21 Jun 2020 16:58:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:28: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:29: 9000000 INFO @ Sun, 21 Jun 2020 16:58:29: #2 number of paired peaks: 587 WARNING @ Sun, 21 Jun 2020 16:58:29: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Sun, 21 Jun 2020 16:58:29: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:29: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:29: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:29: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:29: #2 predicted fragment length is 340 bps INFO @ Sun, 21 Jun 2020 16:58:29: #2 alternative fragment length(s) may be 340 bps INFO @ Sun, 21 Jun 2020 16:58:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.10_model.r INFO @ Sun, 21 Jun 2020 16:58:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:58:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.05_summits.bed INFO @ Sun, 21 Jun 2020 16:58:33: Done! pass1 - making usageList (244 chroms): 2 millis pass2 - checking and writing primary data (4121 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:58:35: 10000000 INFO @ Sun, 21 Jun 2020 16:58:41: 11000000 INFO @ Sun, 21 Jun 2020 16:58:47: 12000000 INFO @ Sun, 21 Jun 2020 16:58:53: 13000000 INFO @ Sun, 21 Jun 2020 16:58:56: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:58:56: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:58:56: #1 total tags in treatment: 13382083 INFO @ Sun, 21 Jun 2020 16:58:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:56: #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 16:58:56: #1 tags after filtering in treatment: 13382057 INFO @ Sun, 21 Jun 2020 16:58:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:56: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:56: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:58:57: #2 number of paired peaks: 587 WARNING @ Sun, 21 Jun 2020 16:58:57: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Sun, 21 Jun 2020 16:58:57: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:57: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:57: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:57: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:57: #2 predicted fragment length is 340 bps INFO @ Sun, 21 Jun 2020 16:58:57: #2 alternative fragment length(s) may be 340 bps INFO @ Sun, 21 Jun 2020 16:58:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.20_model.r INFO @ Sun, 21 Jun 2020 16:58:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:59:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:59:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:59:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:59:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.10_summits.bed INFO @ Sun, 21 Jun 2020 16:59:15: Done! pass1 - making usageList (198 chroms): 1 millis pass2 - checking and writing primary data (3027 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:59:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:59:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:59:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:59:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025462/SRX025462.20_summits.bed INFO @ Sun, 21 Jun 2020 16:59:41: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (1858 records, 4 fields): 7 millis CompletedMACS2peakCalling