Job ID = 6454558 SRX = SRX231909 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:22:30 prefetch.2.10.7: 1) Downloading 'SRR696883'... 2020-06-21T09:22:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:23:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:23:59 prefetch.2.10.7: 'SRR696883' is valid 2020-06-21T09:23:59 prefetch.2.10.7: 1) 'SRR696883' was downloaded successfully Read 9689991 spots for SRR696883/SRR696883.sra Written 9689991 spots for SRR696883/SRR696883.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: 00:00:01 Multiseed full-index search: 00:01:06 9689991 reads; of these: 9689991 (100.00%) were unpaired; of these: 5258129 (54.26%) aligned 0 times 3623212 (37.39%) aligned exactly 1 time 808650 (8.35%) aligned >1 times 45.74% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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_rmdupse_core] 213516 / 4431862 = 0.0482 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 18:27:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.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 18:27:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:27:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:27:11: 1000000 INFO @ Sun, 21 Jun 2020 18:27:16: 2000000 INFO @ Sun, 21 Jun 2020 18:27:21: 3000000 INFO @ Sun, 21 Jun 2020 18:27:27: 4000000 INFO @ Sun, 21 Jun 2020 18:27:28: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:27:28: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:27:28: #1 total tags in treatment: 4218346 INFO @ Sun, 21 Jun 2020 18:27:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:28: #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 18:27:28: #1 tags after filtering in treatment: 4218325 INFO @ Sun, 21 Jun 2020 18:27:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:28: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:29: #2 number of paired peaks: 236 WARNING @ Sun, 21 Jun 2020 18:27:29: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sun, 21 Jun 2020 18:27:29: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:29: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:29: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:29: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:29: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 18:27:29: #2 alternative fragment length(s) may be 3,84,517,545,591 bps INFO @ Sun, 21 Jun 2020 18:27:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.05_model.r INFO @ Sun, 21 Jun 2020 18:27:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:29: #3 Pre-compute pvalue-qvalue table... 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 18:27:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.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 18:27:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:27:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:27:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:27:40: 1000000 INFO @ Sun, 21 Jun 2020 18:27:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:27:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:27:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.05_summits.bed INFO @ Sun, 21 Jun 2020 18:27:44: Done! pass1 - making usageList (220 chroms): 1 millis pass2 - checking and writing primary data (1091 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:27:45: 2000000 INFO @ Sun, 21 Jun 2020 18:27:50: 3000000 INFO @ Sun, 21 Jun 2020 18:27:56: 4000000 INFO @ Sun, 21 Jun 2020 18:27:57: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:27:57: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:27:57: #1 total tags in treatment: 4218346 INFO @ Sun, 21 Jun 2020 18:27:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:57: #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 18:27:57: #1 tags after filtering in treatment: 4218325 INFO @ Sun, 21 Jun 2020 18:27:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:57: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:58: #2 number of paired peaks: 236 WARNING @ Sun, 21 Jun 2020 18:27:58: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sun, 21 Jun 2020 18:27:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:58: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:58: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:58: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 18:27:58: #2 alternative fragment length(s) may be 3,84,517,545,591 bps INFO @ Sun, 21 Jun 2020 18:27:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.10_model.r INFO @ Sun, 21 Jun 2020 18:27:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:58: #3 Pre-compute pvalue-qvalue table... 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 18:28:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.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 18:28:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:28:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:28:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:10: 1000000 INFO @ Sun, 21 Jun 2020 18:28:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.10_summits.bed INFO @ Sun, 21 Jun 2020 18:28:13: Done! pass1 - making usageList (118 chroms): 1 millis pass2 - checking and writing primary data (292 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:28:15: 2000000 INFO @ Sun, 21 Jun 2020 18:28:20: 3000000 INFO @ Sun, 21 Jun 2020 18:28:26: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:28:27: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:28:27: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:28:27: #1 total tags in treatment: 4218346 INFO @ Sun, 21 Jun 2020 18:28:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:27: #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 18:28:27: #1 tags after filtering in treatment: 4218325 INFO @ Sun, 21 Jun 2020 18:28:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:28:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:28:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:28:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:28:28: #2 number of paired peaks: 236 WARNING @ Sun, 21 Jun 2020 18:28:28: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sun, 21 Jun 2020 18:28:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:28:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:28:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:28:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:28:28: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 18:28:28: #2 alternative fragment length(s) may be 3,84,517,545,591 bps INFO @ Sun, 21 Jun 2020 18:28:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.20_model.r INFO @ Sun, 21 Jun 2020 18:28:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:28:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:28:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231909/SRX231909.20_summits.bed INFO @ Sun, 21 Jun 2020 18:28:42: Done! pass1 - making usageList (63 chroms): 0 millis pass2 - checking and writing primary data (105 records, 4 fields): 4 millis CompletedMACS2peakCalling