Job ID = 6458220 SRX = SRX495777 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:17:49 prefetch.2.10.7: 1) Downloading 'SRR1199475'... 2020-06-21T12:17:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:19:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:19:30 prefetch.2.10.7: 'SRR1199475' is valid 2020-06-21T12:19:30 prefetch.2.10.7: 1) 'SRR1199475' was downloaded successfully Read 16315027 spots for SRR1199475/SRR1199475.sra Written 16315027 spots for SRR1199475/SRR1199475.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: 00:05:06 16315027 reads; of these: 16315027 (100.00%) were unpaired; of these: 509362 (3.12%) aligned 0 times 6072522 (37.22%) aligned exactly 1 time 9733143 (59.66%) aligned >1 times 96.88% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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] 6775128 / 15805665 = 0.4287 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 21:28:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.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 21:28:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:28:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:28:52: 1000000 INFO @ Sun, 21 Jun 2020 21:28:56: 2000000 INFO @ Sun, 21 Jun 2020 21:29:01: 3000000 INFO @ Sun, 21 Jun 2020 21:29:06: 4000000 INFO @ Sun, 21 Jun 2020 21:29:10: 5000000 INFO @ Sun, 21 Jun 2020 21:29:15: 6000000 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 21:29:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.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 21:29:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:20: 7000000 INFO @ Sun, 21 Jun 2020 21:29:22: 1000000 INFO @ Sun, 21 Jun 2020 21:29:25: 8000000 INFO @ Sun, 21 Jun 2020 21:29:27: 2000000 INFO @ Sun, 21 Jun 2020 21:29:30: 9000000 INFO @ Sun, 21 Jun 2020 21:29:30: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:29:30: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:29:30: #1 total tags in treatment: 9030537 INFO @ Sun, 21 Jun 2020 21:29:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:30: #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 21:29:30: #1 tags after filtering in treatment: 9030536 INFO @ Sun, 21 Jun 2020 21:29:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:31: #2 number of paired peaks: 2257 INFO @ Sun, 21 Jun 2020 21:29:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:31: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 21:29:31: #2 alternative fragment length(s) may be 2,35,51,568,593 bps INFO @ Sun, 21 Jun 2020 21:29:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.05_model.r WARNING @ Sun, 21 Jun 2020 21:29:31: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:31: #2 You may need to consider one of the other alternative d(s): 2,35,51,568,593 WARNING @ Sun, 21 Jun 2020 21:29:31: #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 21:29:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:32: 3000000 INFO @ Sun, 21 Jun 2020 21:29:36: 4000000 INFO @ Sun, 21 Jun 2020 21:29:41: 5000000 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 21:29:46: 6000000 INFO @ Sun, 21 Jun 2020 21:29:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.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 21:29:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:51: 7000000 INFO @ Sun, 21 Jun 2020 21:29:52: 1000000 INFO @ Sun, 21 Jun 2020 21:29:56: 8000000 INFO @ Sun, 21 Jun 2020 21:29:57: 2000000 INFO @ Sun, 21 Jun 2020 21:29:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.05_summits.bed INFO @ Sun, 21 Jun 2020 21:29:58: Done! pass1 - making usageList (618 chroms): 1 millis pass2 - checking and writing primary data (2255 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:01: 9000000 INFO @ Sun, 21 Jun 2020 21:30:01: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:30:01: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:30:01: #1 total tags in treatment: 9030537 INFO @ Sun, 21 Jun 2020 21:30:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:01: #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 21:30:01: 3000000 INFO @ Sun, 21 Jun 2020 21:30:02: #1 tags after filtering in treatment: 9030536 INFO @ Sun, 21 Jun 2020 21:30:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:02: #2 number of paired peaks: 2257 INFO @ Sun, 21 Jun 2020 21:30:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:02: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 21:30:02: #2 alternative fragment length(s) may be 2,35,51,568,593 bps INFO @ Sun, 21 Jun 2020 21:30:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.10_model.r WARNING @ Sun, 21 Jun 2020 21:30:02: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:02: #2 You may need to consider one of the other alternative d(s): 2,35,51,568,593 WARNING @ Sun, 21 Jun 2020 21:30:02: #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 21:30:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:06: 4000000 INFO @ Sun, 21 Jun 2020 21:30:11: 5000000 INFO @ Sun, 21 Jun 2020 21:30:15: 6000000 INFO @ Sun, 21 Jun 2020 21:30:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:20: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:30:25: 8000000 INFO @ Sun, 21 Jun 2020 21:30:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.10_summits.bed INFO @ Sun, 21 Jun 2020 21:30:29: Done! pass1 - making usageList (293 chroms): 1 millis pass2 - checking and writing primary data (660 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:30: 9000000 INFO @ Sun, 21 Jun 2020 21:30:30: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:30:30: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:30:30: #1 total tags in treatment: 9030537 INFO @ Sun, 21 Jun 2020 21:30:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:30: #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 21:30:31: #1 tags after filtering in treatment: 9030536 INFO @ Sun, 21 Jun 2020 21:30:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:31: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:31: #2 number of paired peaks: 2257 INFO @ Sun, 21 Jun 2020 21:30:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:31: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 21:30:31: #2 alternative fragment length(s) may be 2,35,51,568,593 bps INFO @ Sun, 21 Jun 2020 21:30:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.20_model.r WARNING @ Sun, 21 Jun 2020 21:30:31: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:31: #2 You may need to consider one of the other alternative d(s): 2,35,51,568,593 WARNING @ Sun, 21 Jun 2020 21:30:31: #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 21:30:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:30:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495777/SRX495777.20_summits.bed INFO @ Sun, 21 Jun 2020 21:30:57: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (86 records, 4 fields): 3 millis CompletedMACS2peakCalling