Job ID = 6508746 SRX = SRX467102 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:13:14 prefetch.2.10.7: 1) Downloading 'SRR1164526'... 2020-06-26T15:13:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:15:15 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:15:15 prefetch.2.10.7: 1) 'SRR1164526' was downloaded successfully Read 19299032 spots for SRR1164526/SRR1164526.sra Written 19299032 spots for SRR1164526/SRR1164526.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: 00:04:33 19299032 reads; of these: 19299032 (100.00%) were unpaired; of these: 3492110 (18.09%) aligned 0 times 12552706 (65.04%) aligned exactly 1 time 3254216 (16.86%) aligned >1 times 81.91% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 2381164 / 15806922 = 0.1506 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 @ Sat, 27 Jun 2020 00:25:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.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 @ Sat, 27 Jun 2020 00:25:07: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:25:07: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:25:12: 1000000 INFO @ Sat, 27 Jun 2020 00:25:18: 2000000 INFO @ Sat, 27 Jun 2020 00:25:23: 3000000 INFO @ Sat, 27 Jun 2020 00:25:28: 4000000 INFO @ Sat, 27 Jun 2020 00:25:33: 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 @ Sat, 27 Jun 2020 00:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.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 @ Sat, 27 Jun 2020 00:25:37: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:25:37: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:25:39: 6000000 INFO @ Sat, 27 Jun 2020 00:25:43: 1000000 INFO @ Sat, 27 Jun 2020 00:25:44: 7000000 INFO @ Sat, 27 Jun 2020 00:25:49: 2000000 INFO @ Sat, 27 Jun 2020 00:25:49: 8000000 INFO @ Sat, 27 Jun 2020 00:25:55: 9000000 INFO @ Sat, 27 Jun 2020 00:25:55: 3000000 INFO @ Sat, 27 Jun 2020 00:26:00: 10000000 INFO @ Sat, 27 Jun 2020 00:26:01: 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 @ Sat, 27 Jun 2020 00:26:06: 11000000 INFO @ Sat, 27 Jun 2020 00:26:07: 5000000 INFO @ Sat, 27 Jun 2020 00:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.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 @ Sat, 27 Jun 2020 00:26:07: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:26:07: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:26:11: 12000000 INFO @ Sat, 27 Jun 2020 00:26:13: 1000000 INFO @ Sat, 27 Jun 2020 00:26:13: 6000000 INFO @ Sat, 27 Jun 2020 00:26:16: 13000000 INFO @ Sat, 27 Jun 2020 00:26:18: 2000000 INFO @ Sat, 27 Jun 2020 00:26:19: 7000000 INFO @ Sat, 27 Jun 2020 00:26:19: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:26:19: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:26:19: #1 total tags in treatment: 13425758 INFO @ Sat, 27 Jun 2020 00:26:19: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:26:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:26:19: #1 tags after filtering in treatment: 13425754 INFO @ Sat, 27 Jun 2020 00:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:26:19: #1 finished! INFO @ Sat, 27 Jun 2020 00:26:19: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:26:20: #2 number of paired peaks: 608 WARNING @ Sat, 27 Jun 2020 00:26:20: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Sat, 27 Jun 2020 00:26:20: start model_add_line... INFO @ Sat, 27 Jun 2020 00:26:20: start X-correlation... INFO @ Sat, 27 Jun 2020 00:26:20: end of X-cor INFO @ Sat, 27 Jun 2020 00:26:20: #2 finished! INFO @ Sat, 27 Jun 2020 00:26:20: #2 predicted fragment length is 156 bps INFO @ Sat, 27 Jun 2020 00:26:20: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 27 Jun 2020 00:26:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.05_model.r INFO @ Sat, 27 Jun 2020 00:26:20: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:26:24: 3000000 INFO @ Sat, 27 Jun 2020 00:26:25: 8000000 INFO @ Sat, 27 Jun 2020 00:26:29: 4000000 INFO @ Sat, 27 Jun 2020 00:26:31: 9000000 INFO @ Sat, 27 Jun 2020 00:26:34: 5000000 INFO @ Sat, 27 Jun 2020 00:26:36: 10000000 INFO @ Sat, 27 Jun 2020 00:26:40: 6000000 INFO @ Sat, 27 Jun 2020 00:26:43: 11000000 INFO @ Sat, 27 Jun 2020 00:26:45: 7000000 INFO @ Sat, 27 Jun 2020 00:26:49: 12000000 INFO @ Sat, 27 Jun 2020 00:26:50: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:26:50: 8000000 INFO @ Sat, 27 Jun 2020 00:26:55: 13000000 INFO @ Sat, 27 Jun 2020 00:26:56: 9000000 INFO @ Sat, 27 Jun 2020 00:26:58: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:26:58: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:26:58: #1 total tags in treatment: 13425758 INFO @ Sat, 27 Jun 2020 00:26:58: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:26:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:26:58: #1 tags after filtering in treatment: 13425754 INFO @ Sat, 27 Jun 2020 00:26:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:26:58: #1 finished! INFO @ Sat, 27 Jun 2020 00:26:58: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:26:59: #2 number of paired peaks: 608 WARNING @ Sat, 27 Jun 2020 00:26:59: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Sat, 27 Jun 2020 00:26:59: start model_add_line... INFO @ Sat, 27 Jun 2020 00:26:59: start X-correlation... INFO @ Sat, 27 Jun 2020 00:26:59: end of X-cor INFO @ Sat, 27 Jun 2020 00:26:59: #2 finished! INFO @ Sat, 27 Jun 2020 00:26:59: #2 predicted fragment length is 156 bps INFO @ Sat, 27 Jun 2020 00:26:59: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 27 Jun 2020 00:26:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.10_model.r INFO @ Sat, 27 Jun 2020 00:26:59: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:26:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:27:01: 10000000 INFO @ Sat, 27 Jun 2020 00:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.05_summits.bed INFO @ Sat, 27 Jun 2020 00:27:05: Done! pass1 - making usageList (522 chroms): 2 millis pass2 - checking and writing primary data (5960 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:27:07: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:27:12: 12000000 INFO @ Sat, 27 Jun 2020 00:27:17: 13000000 INFO @ Sat, 27 Jun 2020 00:27:19: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:27:19: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:27:19: #1 total tags in treatment: 13425758 INFO @ Sat, 27 Jun 2020 00:27:19: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:27:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:27:20: #1 tags after filtering in treatment: 13425754 INFO @ Sat, 27 Jun 2020 00:27:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:27:20: #1 finished! INFO @ Sat, 27 Jun 2020 00:27:20: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:27:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:27:21: #2 number of paired peaks: 608 WARNING @ Sat, 27 Jun 2020 00:27:21: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Sat, 27 Jun 2020 00:27:21: start model_add_line... INFO @ Sat, 27 Jun 2020 00:27:21: start X-correlation... INFO @ Sat, 27 Jun 2020 00:27:21: end of X-cor INFO @ Sat, 27 Jun 2020 00:27:21: #2 finished! INFO @ Sat, 27 Jun 2020 00:27:21: #2 predicted fragment length is 156 bps INFO @ Sat, 27 Jun 2020 00:27:21: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 27 Jun 2020 00:27:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.20_model.r INFO @ Sat, 27 Jun 2020 00:27:21: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:27:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:27:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:27:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:27:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:27:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.10_summits.bed INFO @ Sat, 27 Jun 2020 00:27:46: Done! pass1 - making usageList (457 chroms): 1 millis pass2 - checking and writing primary data (4224 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:27:51: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:28:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:28:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:28:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467102/SRX467102.20_summits.bed INFO @ Sat, 27 Jun 2020 00:28:07: Done! pass1 - making usageList (374 chroms): 1 millis pass2 - checking and writing primary data (2440 records, 4 fields): 14 millis CompletedMACS2peakCalling