Job ID = 14519469 SRX = SRX9689633 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 29671210 spots for SRR13258850/SRR13258850.sra Written 29671210 spots for SRR13258850/SRR13258850.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: 00:14:22 29671210 reads; of these: 29671210 (100.00%) were unpaired; of these: 26791 (0.09%) aligned 0 times 25956815 (87.48%) aligned exactly 1 time 3687604 (12.43%) aligned >1 times 99.91% overall alignment rate Time searching: 00:14:23 Overall time: 00:14:23 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] 635 / 29644419 = 0.0000 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 15:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.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 15:15:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 15:15:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 15:15:24: 1000000 INFO @ Sat, 15 Jan 2022 15:15:29: 2000000 INFO @ Sat, 15 Jan 2022 15:15:35: 3000000 INFO @ Sat, 15 Jan 2022 15:15:40: 4000000 INFO @ Sat, 15 Jan 2022 15:15:46: 5000000 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 15:15:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.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 15:15:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 15:15:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 15:15:52: 6000000 INFO @ Sat, 15 Jan 2022 15:15:55: 1000000 INFO @ Sat, 15 Jan 2022 15:15:58: 7000000 INFO @ Sat, 15 Jan 2022 15:16:01: 2000000 INFO @ Sat, 15 Jan 2022 15:16:04: 8000000 INFO @ Sat, 15 Jan 2022 15:16:07: 3000000 INFO @ Sat, 15 Jan 2022 15:16:11: 9000000 INFO @ Sat, 15 Jan 2022 15:16:14: 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 15:16:17: 10000000 INFO @ Sat, 15 Jan 2022 15:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.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 15:16:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 15:16:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 15:16:20: 5000000 INFO @ Sat, 15 Jan 2022 15:16:23: 11000000 INFO @ Sat, 15 Jan 2022 15:16:25: 1000000 INFO @ Sat, 15 Jan 2022 15:16:26: 6000000 INFO @ Sat, 15 Jan 2022 15:16:30: 12000000 INFO @ Sat, 15 Jan 2022 15:16:31: 2000000 INFO @ Sat, 15 Jan 2022 15:16:33: 7000000 INFO @ Sat, 15 Jan 2022 15:16:36: 13000000 INFO @ Sat, 15 Jan 2022 15:16:38: 3000000 INFO @ Sat, 15 Jan 2022 15:16:39: 8000000 INFO @ Sat, 15 Jan 2022 15:16:42: 14000000 INFO @ Sat, 15 Jan 2022 15:16:44: 4000000 INFO @ Sat, 15 Jan 2022 15:16:45: 9000000 INFO @ Sat, 15 Jan 2022 15:16:49: 15000000 INFO @ Sat, 15 Jan 2022 15:16:50: 5000000 INFO @ Sat, 15 Jan 2022 15:16:51: 10000000 INFO @ Sat, 15 Jan 2022 15:16:55: 16000000 INFO @ Sat, 15 Jan 2022 15:16:57: 6000000 INFO @ Sat, 15 Jan 2022 15:16:58: 11000000 INFO @ Sat, 15 Jan 2022 15:17:02: 17000000 INFO @ Sat, 15 Jan 2022 15:17:03: 7000000 INFO @ Sat, 15 Jan 2022 15:17:04: 12000000 INFO @ Sat, 15 Jan 2022 15:17:08: 18000000 INFO @ Sat, 15 Jan 2022 15:17:09: 8000000 INFO @ Sat, 15 Jan 2022 15:17:10: 13000000 INFO @ Sat, 15 Jan 2022 15:17:14: 19000000 INFO @ Sat, 15 Jan 2022 15:17:16: 9000000 INFO @ Sat, 15 Jan 2022 15:17:17: 14000000 INFO @ Sat, 15 Jan 2022 15:17:21: 20000000 INFO @ Sat, 15 Jan 2022 15:17:22: 10000000 INFO @ Sat, 15 Jan 2022 15:17:23: 15000000 INFO @ Sat, 15 Jan 2022 15:17:27: 21000000 INFO @ Sat, 15 Jan 2022 15:17:28: 11000000 INFO @ Sat, 15 Jan 2022 15:17:29: 16000000 INFO @ Sat, 15 Jan 2022 15:17:33: 22000000 INFO @ Sat, 15 Jan 2022 15:17:35: 12000000 INFO @ Sat, 15 Jan 2022 15:17:36: 17000000 INFO @ Sat, 15 Jan 2022 15:17:40: 23000000 INFO @ Sat, 15 Jan 2022 15:17:41: 13000000 INFO @ Sat, 15 Jan 2022 15:17:42: 18000000 INFO @ Sat, 15 Jan 2022 15:17:46: 24000000 INFO @ Sat, 15 Jan 2022 15:17:47: 14000000 INFO @ Sat, 15 Jan 2022 15:17:48: 19000000 INFO @ Sat, 15 Jan 2022 15:17:53: 25000000 INFO @ Sat, 15 Jan 2022 15:17:54: 15000000 INFO @ Sat, 15 Jan 2022 15:17:55: 20000000 INFO @ Sat, 15 Jan 2022 15:17:59: 26000000 INFO @ Sat, 15 Jan 2022 15:18:00: 16000000 INFO @ Sat, 15 Jan 2022 15:18:01: 21000000 INFO @ Sat, 15 Jan 2022 15:18:05: 27000000 INFO @ Sat, 15 Jan 2022 15:18:07: 17000000 INFO @ Sat, 15 Jan 2022 15:18:07: 22000000 INFO @ Sat, 15 Jan 2022 15:18:12: 28000000 INFO @ Sat, 15 Jan 2022 15:18:13: 18000000 INFO @ Sat, 15 Jan 2022 15:18:14: 23000000 INFO @ Sat, 15 Jan 2022 15:18:18: 29000000 INFO @ Sat, 15 Jan 2022 15:18:19: 19000000 INFO @ Sat, 15 Jan 2022 15:18:20: 24000000 INFO @ Sat, 15 Jan 2022 15:18:22: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 15:18:22: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 15:18:22: #1 total tags in treatment: 29643784 INFO @ Sat, 15 Jan 2022 15:18:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 15:18:22: #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 15:18:23: #1 tags after filtering in treatment: 29643646 INFO @ Sat, 15 Jan 2022 15:18:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 15:18:23: #1 finished! INFO @ Sat, 15 Jan 2022 15:18:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 15:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 15:18:25: #2 number of paired peaks: 1364 INFO @ Sat, 15 Jan 2022 15:18:25: start model_add_line... INFO @ Sat, 15 Jan 2022 15:18:26: 20000000 INFO @ Sat, 15 Jan 2022 15:18:26: start X-correlation... INFO @ Sat, 15 Jan 2022 15:18:26: end of X-cor INFO @ Sat, 15 Jan 2022 15:18:26: #2 finished! INFO @ Sat, 15 Jan 2022 15:18:26: #2 predicted fragment length is 54 bps INFO @ Sat, 15 Jan 2022 15:18:26: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 15 Jan 2022 15:18:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.05_model.r WARNING @ Sat, 15 Jan 2022 15:18:26: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 15:18:26: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 15 Jan 2022 15:18:26: #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 15:18:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 15:18:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 15:18:26: 25000000 INFO @ Sat, 15 Jan 2022 15:18:32: 21000000 INFO @ Sat, 15 Jan 2022 15:18:33: 26000000 INFO @ Sat, 15 Jan 2022 15:18:38: 22000000 INFO @ Sat, 15 Jan 2022 15:18:39: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 15:18:44: 23000000 INFO @ Sat, 15 Jan 2022 15:18:45: 28000000 INFO @ Sat, 15 Jan 2022 15:18:51: 24000000 INFO @ Sat, 15 Jan 2022 15:18:52: 29000000 INFO @ Sat, 15 Jan 2022 15:18:56: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 15:18:56: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 15:18:56: #1 total tags in treatment: 29643784 INFO @ Sat, 15 Jan 2022 15:18:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 15:18:56: #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 15:18:56: #1 tags after filtering in treatment: 29643646 INFO @ Sat, 15 Jan 2022 15:18:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 15:18:56: #1 finished! INFO @ Sat, 15 Jan 2022 15:18:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 15:18:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 15:18:57: 25000000 INFO @ Sat, 15 Jan 2022 15:18:59: #2 number of paired peaks: 1364 INFO @ Sat, 15 Jan 2022 15:18:59: start model_add_line... INFO @ Sat, 15 Jan 2022 15:18:59: start X-correlation... INFO @ Sat, 15 Jan 2022 15:18:59: end of X-cor INFO @ Sat, 15 Jan 2022 15:18:59: #2 finished! INFO @ Sat, 15 Jan 2022 15:18:59: #2 predicted fragment length is 54 bps INFO @ Sat, 15 Jan 2022 15:18:59: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 15 Jan 2022 15:18:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.10_model.r WARNING @ Sat, 15 Jan 2022 15:18:59: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 15:18:59: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 15 Jan 2022 15:18:59: #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 15:18:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 15:18:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 15:19:02: 26000000 INFO @ Sat, 15 Jan 2022 15:19:08: 27000000 INFO @ Sat, 15 Jan 2022 15:19:13: 28000000 INFO @ Sat, 15 Jan 2022 15:19:19: 29000000 INFO @ Sat, 15 Jan 2022 15:19:23: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 15:19:23: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 15:19:23: #1 total tags in treatment: 29643784 INFO @ Sat, 15 Jan 2022 15:19:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 15:19:23: #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 15:19:23: #1 tags after filtering in treatment: 29643646 INFO @ Sat, 15 Jan 2022 15:19:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 15:19:23: #1 finished! INFO @ Sat, 15 Jan 2022 15:19:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 15:19:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 15:19:26: #2 number of paired peaks: 1364 INFO @ Sat, 15 Jan 2022 15:19:26: start model_add_line... INFO @ Sat, 15 Jan 2022 15:19:26: start X-correlation... INFO @ Sat, 15 Jan 2022 15:19:26: end of X-cor INFO @ Sat, 15 Jan 2022 15:19:26: #2 finished! INFO @ Sat, 15 Jan 2022 15:19:26: #2 predicted fragment length is 54 bps INFO @ Sat, 15 Jan 2022 15:19:26: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 15 Jan 2022 15:19:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.20_model.r WARNING @ Sat, 15 Jan 2022 15:19:26: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 15:19:26: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 15 Jan 2022 15:19:26: #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 15:19:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 15:19:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 15:19:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 15:20:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 15:20:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.05_peaks.xls INFO @ Sat, 15 Jan 2022 15:20:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 15:20:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.05_summits.bed INFO @ Sat, 15 Jan 2022 15:20:04: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (753 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 15:20:29: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 15:20:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.10_peaks.xls INFO @ Sat, 15 Jan 2022 15:20:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 15:20:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.10_summits.bed INFO @ Sat, 15 Jan 2022 15:20:34: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 15:21:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.20_peaks.xls INFO @ Sat, 15 Jan 2022 15:21:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 15:21:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9689633/SRX9689633.20_summits.bed INFO @ Sat, 15 Jan 2022 15:21:03: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 1 millis CompletedMACS2peakCalling