Job ID = 5790648 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 40,706,036 reads read : 81,412,072 reads written : 40,706,036 reads 0-length : 40,706,036 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 03:08:31 40706036 reads; of these: 40706036 (100.00%) were unpaired; of these: 24501590 (60.19%) aligned 0 times 6659367 (16.36%) aligned exactly 1 time 9545079 (23.45%) aligned >1 times 39.81% overall alignment rate Time searching: 03:08:34 Overall time: 03:08:34 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] 2869582 / 16204446 = 0.1771 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 08:33:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.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 08:33:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:33:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:34:04: 1000000 INFO @ Wed, 22 Apr 2020 08:34:10: 2000000 INFO @ Wed, 22 Apr 2020 08:34:17: 3000000 INFO @ Wed, 22 Apr 2020 08:34:23: 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 08:34:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.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 08:34:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:34:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:34:29: 5000000 INFO @ Wed, 22 Apr 2020 08:34:35: 1000000 INFO @ Wed, 22 Apr 2020 08:34:36: 6000000 INFO @ Wed, 22 Apr 2020 08:34:43: 7000000 INFO @ Wed, 22 Apr 2020 08:34:44: 2000000 INFO @ Wed, 22 Apr 2020 08:34:50: 8000000 INFO @ Wed, 22 Apr 2020 08:34:52: 3000000 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 08:34:57: 9000000 INFO @ Wed, 22 Apr 2020 08:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.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 08:34:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:34:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:35:00: 4000000 INFO @ Wed, 22 Apr 2020 08:35:04: 10000000 INFO @ Wed, 22 Apr 2020 08:35:05: 1000000 INFO @ Wed, 22 Apr 2020 08:35:08: 5000000 INFO @ Wed, 22 Apr 2020 08:35:10: 11000000 INFO @ Wed, 22 Apr 2020 08:35:14: 2000000 INFO @ Wed, 22 Apr 2020 08:35:16: 6000000 INFO @ Wed, 22 Apr 2020 08:35:17: 12000000 INFO @ Wed, 22 Apr 2020 08:35:22: 3000000 INFO @ Wed, 22 Apr 2020 08:35:24: 7000000 INFO @ Wed, 22 Apr 2020 08:35:24: 13000000 INFO @ Wed, 22 Apr 2020 08:35:27: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 08:35:27: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 08:35:27: #1 total tags in treatment: 13334864 INFO @ Wed, 22 Apr 2020 08:35:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:35:27: #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 08:35:27: #1 tags after filtering in treatment: 13334689 INFO @ Wed, 22 Apr 2020 08:35:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:35:27: #1 finished! INFO @ Wed, 22 Apr 2020 08:35:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:35:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:35:30: 4000000 INFO @ Wed, 22 Apr 2020 08:35:31: #2 number of paired peaks: 113823 INFO @ Wed, 22 Apr 2020 08:35:31: start model_add_line... INFO @ Wed, 22 Apr 2020 08:35:31: start X-correlation... INFO @ Wed, 22 Apr 2020 08:35:31: end of X-cor INFO @ Wed, 22 Apr 2020 08:35:31: #2 finished! INFO @ Wed, 22 Apr 2020 08:35:31: #2 predicted fragment length is 109 bps INFO @ Wed, 22 Apr 2020 08:35:31: #2 alternative fragment length(s) may be 109 bps INFO @ Wed, 22 Apr 2020 08:35:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.05_model.r WARNING @ Wed, 22 Apr 2020 08:35:31: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:35:31: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Wed, 22 Apr 2020 08:35:31: #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 08:35:31: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:35:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:35:32: 8000000 INFO @ Wed, 22 Apr 2020 08:35:39: 5000000 INFO @ Wed, 22 Apr 2020 08:35:41: 9000000 INFO @ Wed, 22 Apr 2020 08:35:47: 6000000 INFO @ Wed, 22 Apr 2020 08:35:49: 10000000 INFO @ Wed, 22 Apr 2020 08:35:55: 7000000 INFO @ Wed, 22 Apr 2020 08:35:57: 11000000 INFO @ Wed, 22 Apr 2020 08:36:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:36:03: 8000000 INFO @ Wed, 22 Apr 2020 08:36:05: 12000000 INFO @ Wed, 22 Apr 2020 08:36:11: 9000000 INFO @ Wed, 22 Apr 2020 08:36:13: 13000000 INFO @ Wed, 22 Apr 2020 08:36:16: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 08:36:16: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 08:36:16: #1 total tags in treatment: 13334864 INFO @ Wed, 22 Apr 2020 08:36:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:36:16: #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 08:36:16: #1 tags after filtering in treatment: 13334689 INFO @ Wed, 22 Apr 2020 08:36:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:36:16: #1 finished! INFO @ Wed, 22 Apr 2020 08:36:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:36:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:36:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:36:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.05_summits.bed INFO @ Wed, 22 Apr 2020 08:36:19: Done! INFO @ Wed, 22 Apr 2020 08:36:19: 10000000 pass1 - making usageList (136 chroms): 5 millis pass2 - checking and writing primary data (33093 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:36:20: #2 number of paired peaks: 113823 INFO @ Wed, 22 Apr 2020 08:36:20: start model_add_line... INFO @ Wed, 22 Apr 2020 08:36:20: start X-correlation... INFO @ Wed, 22 Apr 2020 08:36:20: end of X-cor INFO @ Wed, 22 Apr 2020 08:36:20: #2 finished! INFO @ Wed, 22 Apr 2020 08:36:20: #2 predicted fragment length is 109 bps INFO @ Wed, 22 Apr 2020 08:36:20: #2 alternative fragment length(s) may be 109 bps INFO @ Wed, 22 Apr 2020 08:36:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.10_model.r WARNING @ Wed, 22 Apr 2020 08:36:20: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:36:20: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Wed, 22 Apr 2020 08:36:20: #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 08:36:20: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:36:27: 11000000 INFO @ Wed, 22 Apr 2020 08:36:34: 12000000 INFO @ Wed, 22 Apr 2020 08:36:42: 13000000 INFO @ Wed, 22 Apr 2020 08:36:44: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 08:36:44: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 08:36:44: #1 total tags in treatment: 13334864 INFO @ Wed, 22 Apr 2020 08:36:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:36:44: #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 08:36:45: #1 tags after filtering in treatment: 13334689 INFO @ Wed, 22 Apr 2020 08:36:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:36:45: #1 finished! INFO @ Wed, 22 Apr 2020 08:36:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:36:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:36:48: #2 number of paired peaks: 113823 INFO @ Wed, 22 Apr 2020 08:36:48: start model_add_line... INFO @ Wed, 22 Apr 2020 08:36:48: start X-correlation... INFO @ Wed, 22 Apr 2020 08:36:48: end of X-cor INFO @ Wed, 22 Apr 2020 08:36:48: #2 finished! INFO @ Wed, 22 Apr 2020 08:36:48: #2 predicted fragment length is 109 bps INFO @ Wed, 22 Apr 2020 08:36:48: #2 alternative fragment length(s) may be 109 bps INFO @ Wed, 22 Apr 2020 08:36:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.20_model.r WARNING @ Wed, 22 Apr 2020 08:36:48: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:36:48: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Wed, 22 Apr 2020 08:36:48: #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 08:36:48: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:36:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:36:51: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:37:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:37:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:37:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.10_summits.bed INFO @ Wed, 22 Apr 2020 08:37:06: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (7615 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:37:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:37:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:37:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:37:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299291/SRX5299291.20_summits.bed INFO @ Wed, 22 Apr 2020 08:37:34: Done! pass1 - making usageList (43 chroms): 0 millis pass2 - checking and writing primary data (971 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。