Job ID = 5790801 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,080,043 reads read : 32,160,086 reads written : 16,080,043 reads 0-length : 16,080,043 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:03 Time loading mirror index: 00:00:04 Multiseed full-index search: 00:11:28 16080043 reads; of these: 16080043 (100.00%) were unpaired; of these: 3830821 (23.82%) aligned 0 times 8766944 (54.52%) aligned exactly 1 time 3482278 (21.66%) aligned >1 times 76.18% overall alignment rate Time searching: 00:11:36 Overall time: 00:11:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 900505 / 12249222 = 0.0735 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 @ Wed, 22 Apr 2020 07:47:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 07:47:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:47:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:47:39: 1000000 INFO @ Wed, 22 Apr 2020 07:47:46: 2000000 INFO @ Wed, 22 Apr 2020 07:47:53: 3000000 INFO @ Wed, 22 Apr 2020 07:47:59: 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 @ Wed, 22 Apr 2020 07:48:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 07:48:02: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:48:02: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:48:06: 5000000 INFO @ Wed, 22 Apr 2020 07:48:09: 1000000 INFO @ Wed, 22 Apr 2020 07:48:13: 6000000 INFO @ Wed, 22 Apr 2020 07:48:16: 2000000 INFO @ Wed, 22 Apr 2020 07:48:20: 7000000 INFO @ Wed, 22 Apr 2020 07:48:23: 3000000 INFO @ Wed, 22 Apr 2020 07:48:27: 8000000 INFO @ Wed, 22 Apr 2020 07:48:29: 4000000 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 @ Wed, 22 Apr 2020 07:48:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 07:48:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:48:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:48:34: 9000000 INFO @ Wed, 22 Apr 2020 07:48:36: 5000000 INFO @ Wed, 22 Apr 2020 07:48:39: 1000000 INFO @ Wed, 22 Apr 2020 07:48:42: 10000000 INFO @ Wed, 22 Apr 2020 07:48:43: 6000000 INFO @ Wed, 22 Apr 2020 07:48:46: 2000000 INFO @ Wed, 22 Apr 2020 07:48:49: 11000000 INFO @ Wed, 22 Apr 2020 07:48:49: 7000000 INFO @ Wed, 22 Apr 2020 07:48:51: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:48:51: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:48:51: #1 total tags in treatment: 11348717 INFO @ Wed, 22 Apr 2020 07:48:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:48:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:48:52: #1 tags after filtering in treatment: 11348504 INFO @ Wed, 22 Apr 2020 07:48:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:48:52: #1 finished! INFO @ Wed, 22 Apr 2020 07:48:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:48:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:48:53: #2 number of paired peaks: 5638 INFO @ Wed, 22 Apr 2020 07:48:53: start model_add_line... INFO @ Wed, 22 Apr 2020 07:48:53: start X-correlation... INFO @ Wed, 22 Apr 2020 07:48:53: end of X-cor INFO @ Wed, 22 Apr 2020 07:48:53: #2 finished! INFO @ Wed, 22 Apr 2020 07:48:53: #2 predicted fragment length is 75 bps INFO @ Wed, 22 Apr 2020 07:48:53: #2 alternative fragment length(s) may be 75,546 bps INFO @ Wed, 22 Apr 2020 07:48:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.05_model.r WARNING @ Wed, 22 Apr 2020 07:48:53: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:48:53: #2 You may need to consider one of the other alternative d(s): 75,546 WARNING @ Wed, 22 Apr 2020 07:48:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:48:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:48:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:48:53: 3000000 INFO @ Wed, 22 Apr 2020 07:48:56: 8000000 INFO @ Wed, 22 Apr 2020 07:49:00: 4000000 INFO @ Wed, 22 Apr 2020 07:49:03: 9000000 INFO @ Wed, 22 Apr 2020 07:49:07: 5000000 INFO @ Wed, 22 Apr 2020 07:49:09: 10000000 INFO @ Wed, 22 Apr 2020 07:49:14: 6000000 INFO @ Wed, 22 Apr 2020 07:49:16: 11000000 INFO @ Wed, 22 Apr 2020 07:49:18: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:49:19: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:49:19: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:49:19: #1 total tags in treatment: 11348717 INFO @ Wed, 22 Apr 2020 07:49:19: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:49:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:49:19: #1 tags after filtering in treatment: 11348504 INFO @ Wed, 22 Apr 2020 07:49:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:49:19: #1 finished! INFO @ Wed, 22 Apr 2020 07:49:19: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:49:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:49:20: #2 number of paired peaks: 5638 INFO @ Wed, 22 Apr 2020 07:49:20: start model_add_line... INFO @ Wed, 22 Apr 2020 07:49:20: start X-correlation... INFO @ Wed, 22 Apr 2020 07:49:20: end of X-cor INFO @ Wed, 22 Apr 2020 07:49:20: #2 finished! INFO @ Wed, 22 Apr 2020 07:49:20: #2 predicted fragment length is 75 bps INFO @ Wed, 22 Apr 2020 07:49:20: #2 alternative fragment length(s) may be 75,546 bps INFO @ Wed, 22 Apr 2020 07:49:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.10_model.r WARNING @ Wed, 22 Apr 2020 07:49:20: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:49:20: #2 You may need to consider one of the other alternative d(s): 75,546 WARNING @ Wed, 22 Apr 2020 07:49:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:49:20: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:49:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:49:21: 7000000 INFO @ Wed, 22 Apr 2020 07:49:28: 8000000 INFO @ Wed, 22 Apr 2020 07:49:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:49:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:49:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.05_summits.bed INFO @ Wed, 22 Apr 2020 07:49:30: Done! pass1 - making usageList (62 chroms): 2 millis pass2 - checking and writing primary data (1014 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:49:35: 9000000 INFO @ Wed, 22 Apr 2020 07:49:42: 10000000 INFO @ Wed, 22 Apr 2020 07:49:46: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:49:48: 11000000 INFO @ Wed, 22 Apr 2020 07:49:51: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 07:49:51: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 07:49:51: #1 total tags in treatment: 11348717 INFO @ Wed, 22 Apr 2020 07:49:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:49:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:49:51: #1 tags after filtering in treatment: 11348504 INFO @ Wed, 22 Apr 2020 07:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:49:51: #1 finished! INFO @ Wed, 22 Apr 2020 07:49:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:49:52: #2 number of paired peaks: 5638 INFO @ Wed, 22 Apr 2020 07:49:52: start model_add_line... INFO @ Wed, 22 Apr 2020 07:49:52: start X-correlation... INFO @ Wed, 22 Apr 2020 07:49:52: end of X-cor INFO @ Wed, 22 Apr 2020 07:49:52: #2 finished! INFO @ Wed, 22 Apr 2020 07:49:52: #2 predicted fragment length is 75 bps INFO @ Wed, 22 Apr 2020 07:49:52: #2 alternative fragment length(s) may be 75,546 bps INFO @ Wed, 22 Apr 2020 07:49:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.20_model.r WARNING @ Wed, 22 Apr 2020 07:49:52: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:49:52: #2 You may need to consider one of the other alternative d(s): 75,546 WARNING @ Wed, 22 Apr 2020 07:49:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:49:52: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:49:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:49:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:49:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:49:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.10_summits.bed INFO @ Wed, 22 Apr 2020 07:49:58: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (591 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:50:17: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:50:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:50:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:50:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625164/SRX7625164.20_summits.bed INFO @ Wed, 22 Apr 2020 07:50:29: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (331 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。