Job ID = 6454187 SRX = SRX186108 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:06:09 prefetch.2.10.7: 1) Downloading 'SRR567585'... 2020-06-21T09:06:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:08:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:08:33 prefetch.2.10.7: 'SRR567585' is valid 2020-06-21T09:08:33 prefetch.2.10.7: 1) 'SRR567585' was downloaded successfully Read 13121810 spots for SRR567585/SRR567585.sra Written 13121810 spots for SRR567585/SRR567585.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: 00:02:17 13121810 reads; of these: 13121810 (100.00%) were unpaired; of these: 3760364 (28.66%) aligned 0 times 6891184 (52.52%) aligned exactly 1 time 2470262 (18.83%) aligned >1 times 71.34% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 2395301 / 9361446 = 0.2559 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 18:13:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.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 18:13:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:13:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:13:43: 1000000 INFO @ Sun, 21 Jun 2020 18:13:48: 2000000 INFO @ Sun, 21 Jun 2020 18:13:54: 3000000 INFO @ Sun, 21 Jun 2020 18:13:59: 4000000 INFO @ Sun, 21 Jun 2020 18:14:04: 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 18:14:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.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 18:14:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:10: 6000000 INFO @ Sun, 21 Jun 2020 18:14:13: 1000000 INFO @ Sun, 21 Jun 2020 18:14:15: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:14:15: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:14:15: #1 total tags in treatment: 6966145 INFO @ Sun, 21 Jun 2020 18:14:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:15: #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 18:14:15: #1 tags after filtering in treatment: 6966145 INFO @ Sun, 21 Jun 2020 18:14:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:16: #2 number of paired peaks: 846 WARNING @ Sun, 21 Jun 2020 18:14:16: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Sun, 21 Jun 2020 18:14:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:16: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 18:14:16: #2 alternative fragment length(s) may be 4,77,205,246,432,534 bps INFO @ Sun, 21 Jun 2020 18:14:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.05_model.r INFO @ Sun, 21 Jun 2020 18:14:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:14:17: 2000000 INFO @ Sun, 21 Jun 2020 18:14:22: 3000000 INFO @ Sun, 21 Jun 2020 18:14:26: 4000000 INFO @ Sun, 21 Jun 2020 18:14:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:14:31: 5000000 INFO @ Sun, 21 Jun 2020 18:14:35: 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 18:14:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:14:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:14:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.05_summits.bed INFO @ Sun, 21 Jun 2020 18:14:38: Done! pass1 - making usageList (585 chroms): 1 millis pass2 - checking and writing primary data (1967 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:14:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:14:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:14:40: #1 total tags in treatment: 6966145 INFO @ Sun, 21 Jun 2020 18:14:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:40: #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 18:14:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.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 18:14:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:40: #1 tags after filtering in treatment: 6966145 INFO @ Sun, 21 Jun 2020 18:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:41: #2 number of paired peaks: 846 WARNING @ Sun, 21 Jun 2020 18:14:41: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Sun, 21 Jun 2020 18:14:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:41: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 18:14:41: #2 alternative fragment length(s) may be 4,77,205,246,432,534 bps INFO @ Sun, 21 Jun 2020 18:14:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.10_model.r INFO @ Sun, 21 Jun 2020 18:14:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:14:45: 1000000 INFO @ Sun, 21 Jun 2020 18:14:50: 2000000 INFO @ Sun, 21 Jun 2020 18:14:55: 3000000 INFO @ Sun, 21 Jun 2020 18:14:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:00: 4000000 INFO @ Sun, 21 Jun 2020 18:15:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.10_summits.bed INFO @ Sun, 21 Jun 2020 18:15:02: Done! pass1 - making usageList (497 chroms): 1 millis pass2 - checking and writing primary data (1684 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:15:05: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:15:10: 6000000 INFO @ Sun, 21 Jun 2020 18:15:16: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:15:16: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:15:16: #1 total tags in treatment: 6966145 INFO @ Sun, 21 Jun 2020 18:15:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:16: #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 18:15:16: #1 tags after filtering in treatment: 6966145 INFO @ Sun, 21 Jun 2020 18:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:17: #2 number of paired peaks: 846 WARNING @ Sun, 21 Jun 2020 18:15:17: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Sun, 21 Jun 2020 18:15:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:17: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 18:15:17: #2 alternative fragment length(s) may be 4,77,205,246,432,534 bps INFO @ Sun, 21 Jun 2020 18:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.20_model.r INFO @ Sun, 21 Jun 2020 18:15:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:15:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX186108/SRX186108.20_summits.bed INFO @ Sun, 21 Jun 2020 18:15:39: Done! pass1 - making usageList (366 chroms): 0 millis pass2 - checking and writing primary data (763 records, 4 fields): 11 millis CompletedMACS2peakCalling