Job ID = 6453516 SRX = SRX124481 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:28:56 prefetch.2.10.7: 1) Downloading 'SRR423937'... 2020-06-21T08:28:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:30:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:30:00 prefetch.2.10.7: 'SRR423937' is valid 2020-06-21T08:30:00 prefetch.2.10.7: 1) 'SRR423937' was downloaded successfully Read 6871525 spots for SRR423937/SRR423937.sra Written 6871525 spots for SRR423937/SRR423937.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: 00:01:07 6871525 reads; of these: 6871525 (100.00%) were unpaired; of these: 280565 (4.08%) aligned 0 times 5304507 (77.20%) aligned exactly 1 time 1286453 (18.72%) aligned >1 times 95.92% 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] 910338 / 6590960 = 0.1381 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 17:33:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.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 17:33:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:33:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:33:42: 1000000 INFO @ Sun, 21 Jun 2020 17:33:48: 2000000 INFO @ Sun, 21 Jun 2020 17:33:54: 3000000 INFO @ Sun, 21 Jun 2020 17:33:58: 4000000 INFO @ Sun, 21 Jun 2020 17:34:04: 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 17:34:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.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 17:34:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:07: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:34:07: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:34:07: #1 total tags in treatment: 5680622 INFO @ Sun, 21 Jun 2020 17:34:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:34:07: #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 17:34:08: #1 tags after filtering in treatment: 5680577 INFO @ Sun, 21 Jun 2020 17:34:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:34:08: #1 finished! INFO @ Sun, 21 Jun 2020 17:34:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:34:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:34:08: #2 number of paired peaks: 913 WARNING @ Sun, 21 Jun 2020 17:34:08: Fewer paired peaks (913) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 913 pairs to build model! INFO @ Sun, 21 Jun 2020 17:34:08: start model_add_line... INFO @ Sun, 21 Jun 2020 17:34:08: start X-correlation... INFO @ Sun, 21 Jun 2020 17:34:09: end of X-cor INFO @ Sun, 21 Jun 2020 17:34:09: #2 finished! INFO @ Sun, 21 Jun 2020 17:34:09: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 17:34:09: #2 alternative fragment length(s) may be 78 bps INFO @ Sun, 21 Jun 2020 17:34:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.05_model.r INFO @ Sun, 21 Jun 2020 17:34:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:34:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:34:11: 1000000 INFO @ Sun, 21 Jun 2020 17:34:15: 2000000 INFO @ Sun, 21 Jun 2020 17:34:20: 3000000 INFO @ Sun, 21 Jun 2020 17:34:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:24: 4000000 INFO @ Sun, 21 Jun 2020 17:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.05_summits.bed INFO @ Sun, 21 Jun 2020 17:34:28: Done! pass1 - making usageList (237 chroms): 2 millis pass2 - checking and writing primary data (2441 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:34:30: 5000000 INFO @ Sun, 21 Jun 2020 17:34:33: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:34:33: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:34:33: #1 total tags in treatment: 5680622 INFO @ Sun, 21 Jun 2020 17:34:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:34:33: #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 17:34:34: #1 tags after filtering in treatment: 5680577 INFO @ Sun, 21 Jun 2020 17:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:34:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:34:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:34:34: #2 number of paired peaks: 913 WARNING @ Sun, 21 Jun 2020 17:34:34: Fewer paired peaks (913) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 913 pairs to build model! INFO @ Sun, 21 Jun 2020 17:34:34: start model_add_line... INFO @ Sun, 21 Jun 2020 17:34:34: start X-correlation... INFO @ Sun, 21 Jun 2020 17:34:34: end of X-cor INFO @ Sun, 21 Jun 2020 17:34:34: #2 finished! INFO @ Sun, 21 Jun 2020 17:34:34: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 17:34:34: #2 alternative fragment length(s) may be 78 bps INFO @ Sun, 21 Jun 2020 17:34:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.10_model.r INFO @ Sun, 21 Jun 2020 17:34:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:34:34: #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 17:34:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.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 17:34:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:41: 1000000 INFO @ Sun, 21 Jun 2020 17:34:45: 2000000 INFO @ Sun, 21 Jun 2020 17:34:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:50: 3000000 INFO @ Sun, 21 Jun 2020 17:34:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.10_summits.bed INFO @ Sun, 21 Jun 2020 17:34:53: Done! pass1 - making usageList (124 chroms): 1 millis pass2 - checking and writing primary data (1119 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:34:54: 4000000 INFO @ Sun, 21 Jun 2020 17:35:00: 5000000 INFO @ Sun, 21 Jun 2020 17:35:03: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:35:03: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:35:03: #1 total tags in treatment: 5680622 INFO @ Sun, 21 Jun 2020 17:35:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:35:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:35:04: #1 tags after filtering in treatment: 5680577 INFO @ Sun, 21 Jun 2020 17:35:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:35:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:35:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:35:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:35:04: #2 number of paired peaks: 913 WARNING @ Sun, 21 Jun 2020 17:35:04: Fewer paired peaks (913) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 913 pairs to build model! INFO @ Sun, 21 Jun 2020 17:35:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:35:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:35:04: end of X-cor INFO @ Sun, 21 Jun 2020 17:35:04: #2 finished! INFO @ Sun, 21 Jun 2020 17:35:04: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 17:35:04: #2 alternative fragment length(s) may be 78 bps INFO @ Sun, 21 Jun 2020 17:35:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.20_model.r INFO @ Sun, 21 Jun 2020 17:35:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:35:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:35:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:35:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:35:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:35:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX124481/SRX124481.20_summits.bed INFO @ Sun, 21 Jun 2020 17:35:22: Done! pass1 - making usageList (69 chroms): 1 millis pass2 - checking and writing primary data (527 records, 4 fields): 6 millis CompletedMACS2peakCalling