Job ID = 6453353 SRX = SRX1120688 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 'SRR2129920'... 2020-06-21T08:28:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:53 prefetch.2.10.7: 1) 'SRR2129920' was downloaded successfully Read 14335390 spots for SRR2129920/SRR2129920.sra Written 14335390 spots for SRR2129920/SRR2129920.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: 00:08:14 14335390 reads; of these: 14335390 (100.00%) were unpaired; of these: 1690697 (11.79%) aligned 0 times 3392003 (23.66%) aligned exactly 1 time 9252690 (64.54%) aligned >1 times 88.21% overall alignment rate Time searching: 00:08:14 Overall time: 00:08:14 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] 3453081 / 12644693 = 0.2731 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 17:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.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 17:47:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:39: 1000000 INFO @ Sun, 21 Jun 2020 17:47:45: 2000000 INFO @ Sun, 21 Jun 2020 17:47:51: 3000000 INFO @ Sun, 21 Jun 2020 17:47:57: 4000000 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 17:48:03: 5000000 INFO @ Sun, 21 Jun 2020 17:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.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 17:48:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:09: 6000000 INFO @ Sun, 21 Jun 2020 17:48:10: 1000000 INFO @ Sun, 21 Jun 2020 17:48:17: 7000000 INFO @ Sun, 21 Jun 2020 17:48:17: 2000000 INFO @ Sun, 21 Jun 2020 17:48:23: 8000000 INFO @ Sun, 21 Jun 2020 17:48:23: 3000000 INFO @ Sun, 21 Jun 2020 17:48:30: 4000000 INFO @ Sun, 21 Jun 2020 17:48:30: 9000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 17:48:31: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:48:31: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:48:31: #1 total tags in treatment: 9191612 INFO @ Sun, 21 Jun 2020 17:48:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 17:48:32: #1 tags after filtering in treatment: 9191545 INFO @ Sun, 21 Jun 2020 17:48:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:32: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:33: #2 number of paired peaks: 7872 INFO @ Sun, 21 Jun 2020 17:48:33: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:33: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:33: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:33: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:33: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 17:48:33: #2 alternative fragment length(s) may be 2,95 bps INFO @ Sun, 21 Jun 2020 17:48:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.05_model.r WARNING @ Sun, 21 Jun 2020 17:48:33: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:48:33: #2 You may need to consider one of the other alternative d(s): 2,95 WARNING @ Sun, 21 Jun 2020 17:48:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:48:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:48:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.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 17:48:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:36: 5000000 INFO @ Sun, 21 Jun 2020 17:48:40: 1000000 INFO @ Sun, 21 Jun 2020 17:48:43: 6000000 INFO @ Sun, 21 Jun 2020 17:48:47: 2000000 INFO @ Sun, 21 Jun 2020 17:48:50: 7000000 INFO @ Sun, 21 Jun 2020 17:48:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:54: 3000000 INFO @ Sun, 21 Jun 2020 17:48:57: 8000000 INFO @ Sun, 21 Jun 2020 17:49:00: 4000000 INFO @ Sun, 21 Jun 2020 17:49:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.05_summits.bed INFO @ Sun, 21 Jun 2020 17:49:02: Done! pass1 - making usageList (1093 chroms): 2 millis pass2 - checking and writing primary data (5098 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:04: 9000000 INFO @ Sun, 21 Jun 2020 17:49:05: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:49:05: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:49:05: #1 total tags in treatment: 9191612 INFO @ Sun, 21 Jun 2020 17:49:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:05: #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 17:49:06: #1 tags after filtering in treatment: 9191545 INFO @ Sun, 21 Jun 2020 17:49:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:06: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:07: 5000000 INFO @ Sun, 21 Jun 2020 17:49:07: #2 number of paired peaks: 7872 INFO @ Sun, 21 Jun 2020 17:49:07: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:07: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:07: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:07: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:07: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 17:49:07: #2 alternative fragment length(s) may be 2,95 bps INFO @ Sun, 21 Jun 2020 17:49:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.10_model.r WARNING @ Sun, 21 Jun 2020 17:49:07: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:49:07: #2 You may need to consider one of the other alternative d(s): 2,95 WARNING @ Sun, 21 Jun 2020 17:49:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:49:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:13: 6000000 INFO @ Sun, 21 Jun 2020 17:49:19: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:49:25: 8000000 INFO @ Sun, 21 Jun 2020 17:49:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:32: 9000000 INFO @ Sun, 21 Jun 2020 17:49:33: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:49:33: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:49:33: #1 total tags in treatment: 9191612 INFO @ Sun, 21 Jun 2020 17:49:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:33: #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 17:49:34: #1 tags after filtering in treatment: 9191545 INFO @ Sun, 21 Jun 2020 17:49:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.10_summits.bed INFO @ Sun, 21 Jun 2020 17:49:35: Done! INFO @ Sun, 21 Jun 2020 17:49:35: #2 number of paired peaks: 7872 INFO @ Sun, 21 Jun 2020 17:49:35: start model_add_line... pass1 - making usageList (891 chroms): 2 millis pass2 - checking and writing primary data (2640 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:35: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 17:49:35: #2 alternative fragment length(s) may be 2,95 bps INFO @ Sun, 21 Jun 2020 17:49:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.20_model.r WARNING @ Sun, 21 Jun 2020 17:49:35: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:49:35: #2 You may need to consider one of the other alternative d(s): 2,95 WARNING @ Sun, 21 Jun 2020 17:49:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:49:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:49:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120688/SRX1120688.20_summits.bed INFO @ Sun, 21 Jun 2020 17:50:02: Done! pass1 - making usageList (656 chroms): 2 millis pass2 - checking and writing primary data (1603 records, 4 fields): 37 millis CompletedMACS2peakCalling