Job ID = 14519605 SRX = SRX6581717 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20471662 spots for SRR9825050/SRR9825050.sra Written 20471662 spots for SRR9825050/SRR9825050.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: 00:26:04 20471662 reads; of these: 20471662 (100.00%) were unpaired; of these: 509600 (2.49%) aligned 0 times 14641962 (71.52%) aligned exactly 1 time 5320100 (25.99%) aligned >1 times 97.51% overall alignment rate Time searching: 00:26:07 Overall time: 00:26:07 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 12 files... [bam_rmdupse_core] 1722894 / 19962062 = 0.0863 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 17:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.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 17:11:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:11:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:11:32: 1000000 INFO @ Sat, 15 Jan 2022 17:11:37: 2000000 INFO @ Sat, 15 Jan 2022 17:11:43: 3000000 INFO @ Sat, 15 Jan 2022 17:11:49: 4000000 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 17:11:55: 5000000 INFO @ Sat, 15 Jan 2022 17:11:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.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 17:11:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:11:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:12:01: 6000000 INFO @ Sat, 15 Jan 2022 17:12:02: 1000000 INFO @ Sat, 15 Jan 2022 17:12:08: 7000000 INFO @ Sat, 15 Jan 2022 17:12:09: 2000000 INFO @ Sat, 15 Jan 2022 17:12:14: 8000000 INFO @ Sat, 15 Jan 2022 17:12:15: 3000000 INFO @ Sat, 15 Jan 2022 17:12:21: 9000000 INFO @ Sat, 15 Jan 2022 17:12:22: 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 17:12:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.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 17:12:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:12:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:12:27: 10000000 INFO @ Sat, 15 Jan 2022 17:12:28: 5000000 INFO @ Sat, 15 Jan 2022 17:12:32: 1000000 INFO @ Sat, 15 Jan 2022 17:12:34: 11000000 INFO @ Sat, 15 Jan 2022 17:12:35: 6000000 INFO @ Sat, 15 Jan 2022 17:12:39: 2000000 INFO @ Sat, 15 Jan 2022 17:12:40: 12000000 INFO @ Sat, 15 Jan 2022 17:12:41: 7000000 INFO @ Sat, 15 Jan 2022 17:12:45: 3000000 INFO @ Sat, 15 Jan 2022 17:12:47: 13000000 INFO @ Sat, 15 Jan 2022 17:12:48: 8000000 INFO @ Sat, 15 Jan 2022 17:12:52: 4000000 INFO @ Sat, 15 Jan 2022 17:12:53: 14000000 INFO @ Sat, 15 Jan 2022 17:12:54: 9000000 INFO @ Sat, 15 Jan 2022 17:12:58: 5000000 INFO @ Sat, 15 Jan 2022 17:13:00: 15000000 INFO @ Sat, 15 Jan 2022 17:13:00: 10000000 INFO @ Sat, 15 Jan 2022 17:13:05: 6000000 INFO @ Sat, 15 Jan 2022 17:13:06: 16000000 INFO @ Sat, 15 Jan 2022 17:13:07: 11000000 INFO @ Sat, 15 Jan 2022 17:13:11: 7000000 INFO @ Sat, 15 Jan 2022 17:13:13: 17000000 INFO @ Sat, 15 Jan 2022 17:13:13: 12000000 INFO @ Sat, 15 Jan 2022 17:13:17: 8000000 INFO @ Sat, 15 Jan 2022 17:13:19: 18000000 INFO @ Sat, 15 Jan 2022 17:13:20: 13000000 INFO @ Sat, 15 Jan 2022 17:13:21: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:13:21: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:13:21: #1 total tags in treatment: 18239168 INFO @ Sat, 15 Jan 2022 17:13:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:13:21: #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 17:13:21: #1 tags after filtering in treatment: 18239021 INFO @ Sat, 15 Jan 2022 17:13:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:13:21: #1 finished! INFO @ Sat, 15 Jan 2022 17:13:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:13:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:13:23: #2 number of paired peaks: 5020 INFO @ Sat, 15 Jan 2022 17:13:23: start model_add_line... INFO @ Sat, 15 Jan 2022 17:13:23: start X-correlation... INFO @ Sat, 15 Jan 2022 17:13:23: end of X-cor INFO @ Sat, 15 Jan 2022 17:13:23: #2 finished! INFO @ Sat, 15 Jan 2022 17:13:23: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:13:23: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 17:13:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.05_model.r WARNING @ Sat, 15 Jan 2022 17:13:23: #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 17:13:23: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 17:13:23: #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 17:13:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:13:24: 9000000 INFO @ Sat, 15 Jan 2022 17:13:26: 14000000 INFO @ Sat, 15 Jan 2022 17:13:30: 10000000 INFO @ Sat, 15 Jan 2022 17:13:33: 15000000 INFO @ Sat, 15 Jan 2022 17:13:37: 11000000 INFO @ Sat, 15 Jan 2022 17:13:39: 16000000 INFO @ Sat, 15 Jan 2022 17:13:43: 12000000 INFO @ Sat, 15 Jan 2022 17:13:46: 17000000 INFO @ Sat, 15 Jan 2022 17:13:50: 13000000 INFO @ Sat, 15 Jan 2022 17:13:52: 18000000 INFO @ Sat, 15 Jan 2022 17:13:54: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:13:54: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:13:54: #1 total tags in treatment: 18239168 INFO @ Sat, 15 Jan 2022 17:13:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:13:54: #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 17:13:54: #1 tags after filtering in treatment: 18239021 INFO @ Sat, 15 Jan 2022 17:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:13:54: #1 finished! INFO @ Sat, 15 Jan 2022 17:13:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:13:56: 14000000 INFO @ Sat, 15 Jan 2022 17:13:56: #2 number of paired peaks: 5020 INFO @ Sat, 15 Jan 2022 17:13:56: start model_add_line... INFO @ Sat, 15 Jan 2022 17:13:56: start X-correlation... INFO @ Sat, 15 Jan 2022 17:13:56: end of X-cor INFO @ Sat, 15 Jan 2022 17:13:56: #2 finished! INFO @ Sat, 15 Jan 2022 17:13:56: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:13:56: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 17:13:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.10_model.r WARNING @ Sat, 15 Jan 2022 17:13:56: #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 17:13:56: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 17:13:56: #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 17:13:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:13:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:14:02: 15000000 INFO @ Sat, 15 Jan 2022 17:14:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:14:08: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:14:14: 17000000 INFO @ Sat, 15 Jan 2022 17:14:20: 18000000 INFO @ Sat, 15 Jan 2022 17:14:21: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:14:21: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:14:21: #1 total tags in treatment: 18239168 INFO @ Sat, 15 Jan 2022 17:14:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:14:21: #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 17:14:22: #1 tags after filtering in treatment: 18239021 INFO @ Sat, 15 Jan 2022 17:14:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:14:22: #1 finished! INFO @ Sat, 15 Jan 2022 17:14:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:14:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:14:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:14:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:14:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.05_summits.bed INFO @ Sat, 15 Jan 2022 17:14:23: Done! INFO @ Sat, 15 Jan 2022 17:14:23: #2 number of paired peaks: 5020 INFO @ Sat, 15 Jan 2022 17:14:23: start model_add_line... INFO @ Sat, 15 Jan 2022 17:14:23: start X-correlation... INFO @ Sat, 15 Jan 2022 17:14:23: end of X-cor INFO @ Sat, 15 Jan 2022 17:14:23: #2 finished! INFO @ Sat, 15 Jan 2022 17:14:23: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:14:23: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 17:14:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.20_model.r WARNING @ Sat, 15 Jan 2022 17:14:23: #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 17:14:23: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 17:14:23: #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 17:14:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:14:23: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1138 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:14:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:14:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:14:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:14:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.10_summits.bed INFO @ Sat, 15 Jan 2022 17:14:56: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (674 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:15:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:15:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:15:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:15:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581717/SRX6581717.20_summits.bed INFO @ Sat, 15 Jan 2022 17:15:24: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (358 records, 4 fields): 13 millis CompletedMACS2peakCalling