Job ID = 14519596 SRX = SRX6581709 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19407325 spots for SRR9825042/SRR9825042.sra Written 19407325 spots for SRR9825042/SRR9825042.sra 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:31:35 19407325 reads; of these: 19407325 (100.00%) were unpaired; of these: 452571 (2.33%) aligned 0 times 13967652 (71.97%) aligned exactly 1 time 4987102 (25.70%) aligned >1 times 97.67% overall alignment rate Time searching: 00:31:39 Overall time: 00:31:39 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] 1358003 / 18954754 = 0.0716 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:08:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.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 @ Sat, 15 Jan 2022 17:08:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:08:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:08:12: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:08:29: 2000000 INFO @ Sat, 15 Jan 2022 17:08:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.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 @ Sat, 15 Jan 2022 17:08:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:08:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:08:43: 3000000 INFO @ Sat, 15 Jan 2022 17:08:49: 1000000 INFO @ Sat, 15 Jan 2022 17:08:53: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:09:01: 2000000 INFO @ Sat, 15 Jan 2022 17:09:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.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 @ Sat, 15 Jan 2022 17:09:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:09:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:09:03: 5000000 INFO @ Sat, 15 Jan 2022 17:09:13: 1000000 INFO @ Sat, 15 Jan 2022 17:09:14: 3000000 INFO @ Sat, 15 Jan 2022 17:09:16: 6000000 INFO @ Sat, 15 Jan 2022 17:09:25: 2000000 INFO @ Sat, 15 Jan 2022 17:09:26: 4000000 INFO @ Sat, 15 Jan 2022 17:09:27: 7000000 INFO @ Sat, 15 Jan 2022 17:09:37: 3000000 INFO @ Sat, 15 Jan 2022 17:09:38: 5000000 INFO @ Sat, 15 Jan 2022 17:09:39: 8000000 INFO @ Sat, 15 Jan 2022 17:09:49: 4000000 INFO @ Sat, 15 Jan 2022 17:09:50: 6000000 INFO @ Sat, 15 Jan 2022 17:09:51: 9000000 INFO @ Sat, 15 Jan 2022 17:10:02: 5000000 INFO @ Sat, 15 Jan 2022 17:10:02: 7000000 INFO @ Sat, 15 Jan 2022 17:10:04: 10000000 INFO @ Sat, 15 Jan 2022 17:10:13: 6000000 INFO @ Sat, 15 Jan 2022 17:10:14: 8000000 INFO @ Sat, 15 Jan 2022 17:10:17: 11000000 INFO @ Sat, 15 Jan 2022 17:10:25: 7000000 INFO @ Sat, 15 Jan 2022 17:10:25: 9000000 INFO @ Sat, 15 Jan 2022 17:10:27: 12000000 INFO @ Sat, 15 Jan 2022 17:10:37: 8000000 INFO @ Sat, 15 Jan 2022 17:10:37: 10000000 INFO @ Sat, 15 Jan 2022 17:10:38: 13000000 INFO @ Sat, 15 Jan 2022 17:10:49: 14000000 INFO @ Sat, 15 Jan 2022 17:10:49: 11000000 INFO @ Sat, 15 Jan 2022 17:10:49: 9000000 INFO @ Sat, 15 Jan 2022 17:10:59: 15000000 INFO @ Sat, 15 Jan 2022 17:11:00: 10000000 INFO @ Sat, 15 Jan 2022 17:11:01: 12000000 INFO @ Sat, 15 Jan 2022 17:11:09: 16000000 INFO @ Sat, 15 Jan 2022 17:11:12: 11000000 INFO @ Sat, 15 Jan 2022 17:11:13: 13000000 INFO @ Sat, 15 Jan 2022 17:11:20: 17000000 INFO @ Sat, 15 Jan 2022 17:11:24: 12000000 INFO @ Sat, 15 Jan 2022 17:11:25: 14000000 INFO @ Sat, 15 Jan 2022 17:11:26: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:11:26: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:11:26: #1 total tags in treatment: 17596751 INFO @ Sat, 15 Jan 2022 17:11:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:11:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:11:27: #1 tags after filtering in treatment: 17596609 INFO @ Sat, 15 Jan 2022 17:11:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:11:27: #1 finished! INFO @ Sat, 15 Jan 2022 17:11:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:11:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:11:29: #2 number of paired peaks: 5470 INFO @ Sat, 15 Jan 2022 17:11:29: start model_add_line... INFO @ Sat, 15 Jan 2022 17:11:29: start X-correlation... INFO @ Sat, 15 Jan 2022 17:11:29: end of X-cor INFO @ Sat, 15 Jan 2022 17:11:29: #2 finished! INFO @ Sat, 15 Jan 2022 17:11:29: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:11:29: #2 alternative fragment length(s) may be 75,548 bps INFO @ Sat, 15 Jan 2022 17:11:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.05_model.r WARNING @ Sat, 15 Jan 2022 17:11:29: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:11:29: #2 You may need to consider one of the other alternative d(s): 75,548 WARNING @ Sat, 15 Jan 2022 17:11:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 17:11:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:11:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:11:36: 13000000 INFO @ Sat, 15 Jan 2022 17:11:37: 15000000 INFO @ Sat, 15 Jan 2022 17:11:47: 14000000 INFO @ Sat, 15 Jan 2022 17:11:48: 16000000 INFO @ Sat, 15 Jan 2022 17:11:59: 15000000 INFO @ Sat, 15 Jan 2022 17:12:00: 17000000 INFO @ Sat, 15 Jan 2022 17:12:07: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:12:07: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:12:07: #1 total tags in treatment: 17596751 INFO @ Sat, 15 Jan 2022 17:12:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:12:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:12:08: #1 tags after filtering in treatment: 17596609 INFO @ Sat, 15 Jan 2022 17:12:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:12:08: #1 finished! INFO @ Sat, 15 Jan 2022 17:12:08: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:12:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:12:10: #2 number of paired peaks: 5470 INFO @ Sat, 15 Jan 2022 17:12:10: start model_add_line... INFO @ Sat, 15 Jan 2022 17:12:10: start X-correlation... INFO @ Sat, 15 Jan 2022 17:12:10: end of X-cor INFO @ Sat, 15 Jan 2022 17:12:10: #2 finished! INFO @ Sat, 15 Jan 2022 17:12:10: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:12:10: #2 alternative fragment length(s) may be 75,548 bps INFO @ Sat, 15 Jan 2022 17:12:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.10_model.r WARNING @ Sat, 15 Jan 2022 17:12:10: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:12:10: #2 You may need to consider one of the other alternative d(s): 75,548 WARNING @ Sat, 15 Jan 2022 17:12:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 17:12:10: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:12:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:12:11: 16000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:12:22: 17000000 INFO @ Sat, 15 Jan 2022 17:12:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:12:28: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:12:28: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:12:28: #1 total tags in treatment: 17596751 INFO @ Sat, 15 Jan 2022 17:12:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:12:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:12:29: #1 tags after filtering in treatment: 17596609 INFO @ Sat, 15 Jan 2022 17:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:12:29: #1 finished! INFO @ Sat, 15 Jan 2022 17:12:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:12:31: #2 number of paired peaks: 5470 INFO @ Sat, 15 Jan 2022 17:12:31: start model_add_line... INFO @ Sat, 15 Jan 2022 17:12:31: start X-correlation... INFO @ Sat, 15 Jan 2022 17:12:31: end of X-cor INFO @ Sat, 15 Jan 2022 17:12:31: #2 finished! INFO @ Sat, 15 Jan 2022 17:12:31: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:12:31: #2 alternative fragment length(s) may be 75,548 bps INFO @ Sat, 15 Jan 2022 17:12:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.20_model.r WARNING @ Sat, 15 Jan 2022 17:12:31: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:12:31: #2 You may need to consider one of the other alternative d(s): 75,548 WARNING @ Sat, 15 Jan 2022 17:12:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 17:12:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:12:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:12:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:12:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.05_summits.bed INFO @ Sat, 15 Jan 2022 17:12:53: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1087 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:13:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:13:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:13:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:13:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:13:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.10_summits.bed INFO @ Sat, 15 Jan 2022 17:13:33: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (620 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:13:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:13:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:13:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581709/SRX6581709.20_summits.bed INFO @ Sat, 15 Jan 2022 17:13:55: Done! pass1 - making usageList (24 chroms): 2 millis pass2 - checking and writing primary data (329 records, 4 fields): 3 millis CompletedMACS2peakCalling