Job ID = 14519547 SRX = SRX9963443 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 36134165 spots for SRR13565223/SRR13565223.sra Written 36134165 spots for SRR13565223/SRR13565223.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: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 01:02:11 36134165 reads; of these: 36134165 (100.00%) were unpaired; of these: 4738933 (13.11%) aligned 0 times 17062384 (47.22%) aligned exactly 1 time 14332848 (39.67%) aligned >1 times 86.89% overall alignment rate Time searching: 01:02:16 Overall time: 01:02:16 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 16 files... [bam_rmdupse_core] 7944422 / 31395232 = 0.2530 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 17:16:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.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 17:16:10: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:16:10: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:16:18: 1000000 INFO @ Sat, 15 Jan 2022 17:16:26: 2000000 INFO @ Sat, 15 Jan 2022 17:16:33: 3000000 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 17:16:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.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 17:16:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:16:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:16:41: 4000000 INFO @ Sat, 15 Jan 2022 17:16:47: 1000000 INFO @ Sat, 15 Jan 2022 17:16:49: 5000000 INFO @ Sat, 15 Jan 2022 17:16:55: 2000000 INFO @ Sat, 15 Jan 2022 17:16:57: 6000000 INFO @ Sat, 15 Jan 2022 17:17:02: 3000000 INFO @ Sat, 15 Jan 2022 17:17:05: 7000000 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 17:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.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 17:17:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:17:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:17:10: 4000000 INFO @ Sat, 15 Jan 2022 17:17:13: 8000000 INFO @ Sat, 15 Jan 2022 17:17:18: 1000000 INFO @ Sat, 15 Jan 2022 17:17:18: 5000000 INFO @ Sat, 15 Jan 2022 17:17:22: 9000000 INFO @ Sat, 15 Jan 2022 17:17:26: 6000000 INFO @ Sat, 15 Jan 2022 17:17:27: 2000000 INFO @ Sat, 15 Jan 2022 17:17:31: 10000000 INFO @ Sat, 15 Jan 2022 17:17:34: 7000000 INFO @ Sat, 15 Jan 2022 17:17:35: 3000000 INFO @ Sat, 15 Jan 2022 17:17:39: 11000000 INFO @ Sat, 15 Jan 2022 17:17:42: 8000000 INFO @ Sat, 15 Jan 2022 17:17:45: 4000000 INFO @ Sat, 15 Jan 2022 17:17:48: 12000000 INFO @ Sat, 15 Jan 2022 17:17:50: 9000000 INFO @ Sat, 15 Jan 2022 17:17:53: 5000000 INFO @ Sat, 15 Jan 2022 17:17:57: 13000000 INFO @ Sat, 15 Jan 2022 17:17:58: 10000000 INFO @ Sat, 15 Jan 2022 17:18:02: 6000000 INFO @ Sat, 15 Jan 2022 17:18:06: 14000000 INFO @ Sat, 15 Jan 2022 17:18:06: 11000000 INFO @ Sat, 15 Jan 2022 17:18:11: 7000000 INFO @ Sat, 15 Jan 2022 17:18:14: 15000000 INFO @ Sat, 15 Jan 2022 17:18:14: 12000000 INFO @ Sat, 15 Jan 2022 17:18:19: 8000000 INFO @ Sat, 15 Jan 2022 17:18:22: 13000000 INFO @ Sat, 15 Jan 2022 17:18:23: 16000000 INFO @ Sat, 15 Jan 2022 17:18:28: 9000000 INFO @ Sat, 15 Jan 2022 17:18:30: 14000000 INFO @ Sat, 15 Jan 2022 17:18:31: 17000000 INFO @ Sat, 15 Jan 2022 17:18:37: 10000000 INFO @ Sat, 15 Jan 2022 17:18:39: 15000000 INFO @ Sat, 15 Jan 2022 17:18:40: 18000000 INFO @ Sat, 15 Jan 2022 17:18:46: 11000000 INFO @ Sat, 15 Jan 2022 17:18:47: 16000000 INFO @ Sat, 15 Jan 2022 17:18:48: 19000000 INFO @ Sat, 15 Jan 2022 17:18:55: 17000000 INFO @ Sat, 15 Jan 2022 17:18:55: 12000000 INFO @ Sat, 15 Jan 2022 17:18:56: 20000000 INFO @ Sat, 15 Jan 2022 17:19:03: 18000000 INFO @ Sat, 15 Jan 2022 17:19:04: 21000000 INFO @ Sat, 15 Jan 2022 17:19:04: 13000000 INFO @ Sat, 15 Jan 2022 17:19:12: 19000000 INFO @ Sat, 15 Jan 2022 17:19:12: 22000000 INFO @ Sat, 15 Jan 2022 17:19:12: 14000000 INFO @ Sat, 15 Jan 2022 17:19:20: 20000000 INFO @ Sat, 15 Jan 2022 17:19:20: 23000000 INFO @ Sat, 15 Jan 2022 17:19:21: 15000000 INFO @ Sat, 15 Jan 2022 17:19:24: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:19:24: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:19:24: #1 total tags in treatment: 23450810 INFO @ Sat, 15 Jan 2022 17:19:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:19:24: #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 17:19:25: #1 tags after filtering in treatment: 23450704 INFO @ Sat, 15 Jan 2022 17:19:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:19:25: #1 finished! INFO @ Sat, 15 Jan 2022 17:19:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:19:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:19:28: 21000000 INFO @ Sat, 15 Jan 2022 17:19:28: #2 number of paired peaks: 49631 INFO @ Sat, 15 Jan 2022 17:19:28: start model_add_line... INFO @ Sat, 15 Jan 2022 17:19:29: start X-correlation... INFO @ Sat, 15 Jan 2022 17:19:29: end of X-cor INFO @ Sat, 15 Jan 2022 17:19:29: #2 finished! INFO @ Sat, 15 Jan 2022 17:19:29: #2 predicted fragment length is 93 bps INFO @ Sat, 15 Jan 2022 17:19:29: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 15 Jan 2022 17:19:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.05_model.r WARNING @ Sat, 15 Jan 2022 17:19:29: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:19:29: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 15 Jan 2022 17:19:29: #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 17:19:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:19:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:19:30: 16000000 INFO @ Sat, 15 Jan 2022 17:19:36: 22000000 INFO @ Sat, 15 Jan 2022 17:19:38: 17000000 INFO @ Sat, 15 Jan 2022 17:19:44: 23000000 INFO @ Sat, 15 Jan 2022 17:19:47: 18000000 INFO @ Sat, 15 Jan 2022 17:19:48: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:19:48: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:19:48: #1 total tags in treatment: 23450810 INFO @ Sat, 15 Jan 2022 17:19:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:19:48: #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 17:19:49: #1 tags after filtering in treatment: 23450704 INFO @ Sat, 15 Jan 2022 17:19:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:19:49: #1 finished! INFO @ Sat, 15 Jan 2022 17:19:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:19:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:19:52: #2 number of paired peaks: 49631 INFO @ Sat, 15 Jan 2022 17:19:52: start model_add_line... INFO @ Sat, 15 Jan 2022 17:19:53: start X-correlation... INFO @ Sat, 15 Jan 2022 17:19:53: end of X-cor INFO @ Sat, 15 Jan 2022 17:19:53: #2 finished! INFO @ Sat, 15 Jan 2022 17:19:53: #2 predicted fragment length is 93 bps INFO @ Sat, 15 Jan 2022 17:19:53: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 15 Jan 2022 17:19:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.10_model.r WARNING @ Sat, 15 Jan 2022 17:19:53: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:19:53: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 15 Jan 2022 17:19:53: #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 17:19:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:19:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:19:54: 19000000 INFO @ Sat, 15 Jan 2022 17:20:02: 20000000 INFO @ Sat, 15 Jan 2022 17:20:10: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:20:18: 22000000 INFO @ Sat, 15 Jan 2022 17:20:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:20:26: 23000000 INFO @ Sat, 15 Jan 2022 17:20:30: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:20:30: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:20:30: #1 total tags in treatment: 23450810 INFO @ Sat, 15 Jan 2022 17:20:30: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:20:30: #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 17:20:31: #1 tags after filtering in treatment: 23450704 INFO @ Sat, 15 Jan 2022 17:20:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:20:31: #1 finished! INFO @ Sat, 15 Jan 2022 17:20:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:20:35: #2 number of paired peaks: 49631 INFO @ Sat, 15 Jan 2022 17:20:35: start model_add_line... INFO @ Sat, 15 Jan 2022 17:20:35: start X-correlation... INFO @ Sat, 15 Jan 2022 17:20:35: end of X-cor INFO @ Sat, 15 Jan 2022 17:20:35: #2 finished! INFO @ Sat, 15 Jan 2022 17:20:35: #2 predicted fragment length is 93 bps INFO @ Sat, 15 Jan 2022 17:20:35: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 15 Jan 2022 17:20:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.20_model.r WARNING @ Sat, 15 Jan 2022 17:20:35: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:20:35: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 15 Jan 2022 17:20:35: #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 17:20:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:20:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:20:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:20:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:20:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:20:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.05_summits.bed INFO @ Sat, 15 Jan 2022 17:20:49: Done! pass1 - making usageList (128 chroms): 2 millis pass2 - checking and writing primary data (7256 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.10_summits.bed INFO @ Sat, 15 Jan 2022 17:21:13: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (2637 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:21:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:21:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:21:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:21:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963443/SRX9963443.20_summits.bed INFO @ Sat, 15 Jan 2022 17:21:58: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (1053 records, 4 fields): 24 millis CompletedMACS2peakCalling