Job ID = 14519545 SRX = SRX9963441 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 43177517 spots for SRR13565221/SRR13565221.sra Written 43177517 spots for SRR13565221/SRR13565221.sra 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:23:45 43177517 reads; of these: 43177517 (100.00%) were unpaired; of these: 6560084 (15.19%) aligned 0 times 17478364 (40.48%) aligned exactly 1 time 19139069 (44.33%) aligned >1 times 84.81% overall alignment rate Time searching: 01:23:46 Overall time: 01:23:46 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] 8895120 / 36617433 = 0.2429 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 17:35:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.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 17:35:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:35:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:35:50: 1000000 INFO @ Sat, 15 Jan 2022 17:35:59: 2000000 INFO @ Sat, 15 Jan 2022 17:36:07: 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 17:36:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.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 17:36:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:36:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:36:15: 4000000 INFO @ Sat, 15 Jan 2022 17:36:23: 5000000 INFO @ Sat, 15 Jan 2022 17:36:24: 1000000 INFO @ Sat, 15 Jan 2022 17:36:32: 6000000 INFO @ Sat, 15 Jan 2022 17:36:36: 2000000 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 17:36:40: 7000000 INFO @ Sat, 15 Jan 2022 17:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.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 17:36:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:36:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:36:47: 3000000 INFO @ Sat, 15 Jan 2022 17:36:48: 8000000 INFO @ Sat, 15 Jan 2022 17:36:54: 1000000 INFO @ Sat, 15 Jan 2022 17:36:56: 9000000 INFO @ Sat, 15 Jan 2022 17:37:00: 4000000 INFO @ Sat, 15 Jan 2022 17:37:05: 10000000 INFO @ Sat, 15 Jan 2022 17:37:06: 2000000 INFO @ Sat, 15 Jan 2022 17:37:11: 5000000 INFO @ Sat, 15 Jan 2022 17:37:13: 11000000 INFO @ Sat, 15 Jan 2022 17:37:17: 3000000 INFO @ Sat, 15 Jan 2022 17:37:21: 12000000 INFO @ Sat, 15 Jan 2022 17:37:23: 6000000 INFO @ Sat, 15 Jan 2022 17:37:29: 4000000 INFO @ Sat, 15 Jan 2022 17:37:30: 13000000 INFO @ Sat, 15 Jan 2022 17:37:35: 7000000 INFO @ Sat, 15 Jan 2022 17:37:38: 14000000 INFO @ Sat, 15 Jan 2022 17:37:40: 5000000 INFO @ Sat, 15 Jan 2022 17:37:47: 15000000 INFO @ Sat, 15 Jan 2022 17:37:47: 8000000 INFO @ Sat, 15 Jan 2022 17:37:51: 6000000 INFO @ Sat, 15 Jan 2022 17:37:55: 16000000 INFO @ Sat, 15 Jan 2022 17:37:59: 9000000 INFO @ Sat, 15 Jan 2022 17:38:03: 7000000 INFO @ Sat, 15 Jan 2022 17:38:04: 17000000 INFO @ Sat, 15 Jan 2022 17:38:10: 10000000 INFO @ Sat, 15 Jan 2022 17:38:12: 18000000 INFO @ Sat, 15 Jan 2022 17:38:14: 8000000 INFO @ Sat, 15 Jan 2022 17:38:20: 19000000 INFO @ Sat, 15 Jan 2022 17:38:21: 11000000 INFO @ Sat, 15 Jan 2022 17:38:25: 9000000 INFO @ Sat, 15 Jan 2022 17:38:28: 20000000 INFO @ Sat, 15 Jan 2022 17:38:31: 12000000 INFO @ Sat, 15 Jan 2022 17:38:35: 10000000 INFO @ Sat, 15 Jan 2022 17:38:37: 21000000 INFO @ Sat, 15 Jan 2022 17:38:43: 13000000 INFO @ Sat, 15 Jan 2022 17:38:45: 22000000 INFO @ Sat, 15 Jan 2022 17:38:46: 11000000 INFO @ Sat, 15 Jan 2022 17:38:52: 23000000 INFO @ Sat, 15 Jan 2022 17:38:55: 14000000 INFO @ Sat, 15 Jan 2022 17:38:57: 12000000 INFO @ Sat, 15 Jan 2022 17:39:01: 24000000 INFO @ Sat, 15 Jan 2022 17:39:06: 15000000 INFO @ Sat, 15 Jan 2022 17:39:07: 13000000 INFO @ Sat, 15 Jan 2022 17:39:09: 25000000 INFO @ Sat, 15 Jan 2022 17:39:17: 16000000 INFO @ Sat, 15 Jan 2022 17:39:17: 14000000 INFO @ Sat, 15 Jan 2022 17:39:17: 26000000 INFO @ Sat, 15 Jan 2022 17:39:26: 27000000 INFO @ Sat, 15 Jan 2022 17:39:28: 17000000 INFO @ Sat, 15 Jan 2022 17:39:29: 15000000 INFO @ Sat, 15 Jan 2022 17:39:32: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:39:32: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:39:32: #1 total tags in treatment: 27722313 INFO @ Sat, 15 Jan 2022 17:39:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:39:32: #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 17:39:33: #1 tags after filtering in treatment: 27722219 INFO @ Sat, 15 Jan 2022 17:39:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:39:33: #1 finished! INFO @ Sat, 15 Jan 2022 17:39:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:39:39: 18000000 INFO @ Sat, 15 Jan 2022 17:39:39: #2 number of paired peaks: 70677 INFO @ Sat, 15 Jan 2022 17:39:39: start model_add_line... INFO @ Sat, 15 Jan 2022 17:39:39: start X-correlation... INFO @ Sat, 15 Jan 2022 17:39:39: end of X-cor INFO @ Sat, 15 Jan 2022 17:39:39: #2 finished! INFO @ Sat, 15 Jan 2022 17:39:39: #2 predicted fragment length is 90 bps INFO @ Sat, 15 Jan 2022 17:39:39: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 15 Jan 2022 17:39:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.05_model.r WARNING @ Sat, 15 Jan 2022 17:39:39: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:39:39: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 15 Jan 2022 17:39:39: #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 17:39:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:39:39: 16000000 INFO @ Sat, 15 Jan 2022 17:39:49: 19000000 INFO @ Sat, 15 Jan 2022 17:39:50: 17000000 INFO @ Sat, 15 Jan 2022 17:40:00: 20000000 INFO @ Sat, 15 Jan 2022 17:40:01: 18000000 INFO @ Sat, 15 Jan 2022 17:40:11: 21000000 INFO @ Sat, 15 Jan 2022 17:40:12: 19000000 INFO @ Sat, 15 Jan 2022 17:40:21: 22000000 INFO @ Sat, 15 Jan 2022 17:40:22: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:40:31: 23000000 INFO @ Sat, 15 Jan 2022 17:40:33: 21000000 INFO @ Sat, 15 Jan 2022 17:40:42: 24000000 INFO @ Sat, 15 Jan 2022 17:40:44: 22000000 INFO @ Sat, 15 Jan 2022 17:40:53: 25000000 INFO @ Sat, 15 Jan 2022 17:40:54: 23000000 INFO @ Sat, 15 Jan 2022 17:41:04: 26000000 INFO @ Sat, 15 Jan 2022 17:41:04: 24000000 INFO @ Sat, 15 Jan 2022 17:41:11: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:41:15: 27000000 INFO @ Sat, 15 Jan 2022 17:41:15: 25000000 INFO @ Sat, 15 Jan 2022 17:41:23: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:41:23: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:41:23: #1 total tags in treatment: 27722313 INFO @ Sat, 15 Jan 2022 17:41:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:41:23: #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 17:41:24: #1 tags after filtering in treatment: 27722219 INFO @ Sat, 15 Jan 2022 17:41:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:41:24: #1 finished! INFO @ Sat, 15 Jan 2022 17:41:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:41:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:41:25: 26000000 INFO @ Sat, 15 Jan 2022 17:41:30: #2 number of paired peaks: 70677 INFO @ Sat, 15 Jan 2022 17:41:30: start model_add_line... INFO @ Sat, 15 Jan 2022 17:41:30: start X-correlation... INFO @ Sat, 15 Jan 2022 17:41:30: end of X-cor INFO @ Sat, 15 Jan 2022 17:41:30: #2 finished! INFO @ Sat, 15 Jan 2022 17:41:30: #2 predicted fragment length is 90 bps INFO @ Sat, 15 Jan 2022 17:41:30: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 15 Jan 2022 17:41:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.10_model.r WARNING @ Sat, 15 Jan 2022 17:41:30: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:41:30: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 15 Jan 2022 17:41:30: #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 17:41:30: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:41:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:41:36: 27000000 INFO @ Sat, 15 Jan 2022 17:41:44: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:41:44: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:41:44: #1 total tags in treatment: 27722313 INFO @ Sat, 15 Jan 2022 17:41:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:41:44: #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 17:41:45: #1 tags after filtering in treatment: 27722219 INFO @ Sat, 15 Jan 2022 17:41:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:41:45: #1 finished! INFO @ Sat, 15 Jan 2022 17:41:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:41:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:41:51: #2 number of paired peaks: 70677 INFO @ Sat, 15 Jan 2022 17:41:51: start model_add_line... INFO @ Sat, 15 Jan 2022 17:41:51: start X-correlation... INFO @ Sat, 15 Jan 2022 17:41:51: end of X-cor INFO @ Sat, 15 Jan 2022 17:41:51: #2 finished! INFO @ Sat, 15 Jan 2022 17:41:51: #2 predicted fragment length is 90 bps INFO @ Sat, 15 Jan 2022 17:41:51: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 15 Jan 2022 17:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.20_model.r WARNING @ Sat, 15 Jan 2022 17:41:51: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:41:51: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 15 Jan 2022 17:41:51: #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 17:41:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:41:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:41:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:41:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.05_summits.bed INFO @ Sat, 15 Jan 2022 17:41:56: Done! pass1 - making usageList (184 chroms): 3 millis pass2 - checking and writing primary data (13174 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:43:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:43:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:43:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:43:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:43:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.10_summits.bed INFO @ Sat, 15 Jan 2022 17:43:56: Done! pass1 - making usageList (114 chroms): 2 millis pass2 - checking and writing primary data (4122 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963441/SRX9963441.20_summits.bed INFO @ Sat, 15 Jan 2022 17:44:24: Done! pass1 - making usageList (63 chroms): 3 millis pass2 - checking and writing primary data (1697 records, 4 fields): 10 millis CompletedMACS2peakCalling