Job ID = 14519549 SRX = SRX9963445 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30182389 spots for SRR13565225/SRR13565225.sra Written 30182389 spots for SRR13565225/SRR13565225.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: 01:27:53 30182389 reads; of these: 30182389 (100.00%) were unpaired; of these: 1364680 (4.52%) aligned 0 times 21880370 (72.49%) aligned exactly 1 time 6937339 (22.98%) aligned >1 times 95.48% overall alignment rate Time searching: 01:27:55 Overall time: 01:27:55 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] 3856959 / 28817709 = 0.1338 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 17:45:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.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 17:45:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:45:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:45:44: 1000000 INFO @ Sat, 15 Jan 2022 17:45:57: 2000000 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 17:46:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.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 17:46:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:46:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:46:09: 3000000 INFO @ Sat, 15 Jan 2022 17:46:10: 1000000 INFO @ Sat, 15 Jan 2022 17:46:18: 2000000 INFO @ Sat, 15 Jan 2022 17:46:22: 4000000 INFO @ Sat, 15 Jan 2022 17:46:26: 3000000 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 17:46:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.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 17:46:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:46:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:46:35: 4000000 INFO @ Sat, 15 Jan 2022 17:46:35: 5000000 INFO @ Sat, 15 Jan 2022 17:46:42: 1000000 INFO @ Sat, 15 Jan 2022 17:46:45: 5000000 INFO @ Sat, 15 Jan 2022 17:46:48: 6000000 INFO @ Sat, 15 Jan 2022 17:46:52: 2000000 INFO @ Sat, 15 Jan 2022 17:46:55: 6000000 INFO @ Sat, 15 Jan 2022 17:47:01: 7000000 INFO @ Sat, 15 Jan 2022 17:47:02: 3000000 INFO @ Sat, 15 Jan 2022 17:47:04: 7000000 INFO @ Sat, 15 Jan 2022 17:47:12: 4000000 INFO @ Sat, 15 Jan 2022 17:47:14: 8000000 INFO @ Sat, 15 Jan 2022 17:47:14: 8000000 INFO @ Sat, 15 Jan 2022 17:47:22: 5000000 INFO @ Sat, 15 Jan 2022 17:47:25: 9000000 INFO @ Sat, 15 Jan 2022 17:47:26: 9000000 INFO @ Sat, 15 Jan 2022 17:47:32: 6000000 INFO @ Sat, 15 Jan 2022 17:47:35: 10000000 INFO @ Sat, 15 Jan 2022 17:47:38: 10000000 INFO @ Sat, 15 Jan 2022 17:47:43: 7000000 INFO @ Sat, 15 Jan 2022 17:47:44: 11000000 INFO @ Sat, 15 Jan 2022 17:47:49: 11000000 INFO @ Sat, 15 Jan 2022 17:47:52: 8000000 INFO @ Sat, 15 Jan 2022 17:47:54: 12000000 INFO @ Sat, 15 Jan 2022 17:48:00: 12000000 INFO @ Sat, 15 Jan 2022 17:48:01: 9000000 INFO @ Sat, 15 Jan 2022 17:48:04: 13000000 INFO @ Sat, 15 Jan 2022 17:48:10: 10000000 INFO @ Sat, 15 Jan 2022 17:48:11: 13000000 INFO @ Sat, 15 Jan 2022 17:48:13: 14000000 INFO @ Sat, 15 Jan 2022 17:48:19: 11000000 INFO @ Sat, 15 Jan 2022 17:48:22: 14000000 INFO @ Sat, 15 Jan 2022 17:48:23: 15000000 INFO @ Sat, 15 Jan 2022 17:48:28: 12000000 INFO @ Sat, 15 Jan 2022 17:48:32: 16000000 INFO @ Sat, 15 Jan 2022 17:48:34: 15000000 INFO @ Sat, 15 Jan 2022 17:48:37: 13000000 INFO @ Sat, 15 Jan 2022 17:48:42: 17000000 INFO @ Sat, 15 Jan 2022 17:48:45: 16000000 INFO @ Sat, 15 Jan 2022 17:48:46: 14000000 INFO @ Sat, 15 Jan 2022 17:48:51: 18000000 INFO @ Sat, 15 Jan 2022 17:48:56: 15000000 INFO @ Sat, 15 Jan 2022 17:48:57: 17000000 INFO @ Sat, 15 Jan 2022 17:49:00: 19000000 INFO @ Sat, 15 Jan 2022 17:49:05: 16000000 INFO @ Sat, 15 Jan 2022 17:49:08: 18000000 INFO @ Sat, 15 Jan 2022 17:49:09: 20000000 INFO @ Sat, 15 Jan 2022 17:49:15: 17000000 INFO @ Sat, 15 Jan 2022 17:49:19: 21000000 INFO @ Sat, 15 Jan 2022 17:49:20: 19000000 INFO @ Sat, 15 Jan 2022 17:49:25: 18000000 INFO @ Sat, 15 Jan 2022 17:49:29: 22000000 INFO @ Sat, 15 Jan 2022 17:49:31: 20000000 INFO @ Sat, 15 Jan 2022 17:49:34: 19000000 INFO @ Sat, 15 Jan 2022 17:49:39: 23000000 INFO @ Sat, 15 Jan 2022 17:49:42: 21000000 INFO @ Sat, 15 Jan 2022 17:49:44: 20000000 INFO @ Sat, 15 Jan 2022 17:49:49: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:49:53: 22000000 INFO @ Sat, 15 Jan 2022 17:49:55: 21000000 INFO @ Sat, 15 Jan 2022 17:49:59: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:49:59: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:49:59: #1 total tags in treatment: 24960750 INFO @ Sat, 15 Jan 2022 17:49:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:49:59: #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 17:50:00: #1 tags after filtering in treatment: 24960639 INFO @ Sat, 15 Jan 2022 17:50:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:50:00: #1 finished! INFO @ Sat, 15 Jan 2022 17:50:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:50:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:50:03: #2 number of paired peaks: 6992 INFO @ Sat, 15 Jan 2022 17:50:03: start model_add_line... INFO @ Sat, 15 Jan 2022 17:50:03: start X-correlation... INFO @ Sat, 15 Jan 2022 17:50:03: end of X-cor INFO @ Sat, 15 Jan 2022 17:50:03: #2 finished! INFO @ Sat, 15 Jan 2022 17:50:03: #2 predicted fragment length is 79 bps INFO @ Sat, 15 Jan 2022 17:50:03: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 15 Jan 2022 17:50:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.10_model.r WARNING @ Sat, 15 Jan 2022 17:50:03: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:50:03: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Sat, 15 Jan 2022 17:50:03: #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 17:50:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:50:04: 23000000 INFO @ Sat, 15 Jan 2022 17:50:05: 22000000 INFO @ Sat, 15 Jan 2022 17:50:14: 23000000 INFO @ Sat, 15 Jan 2022 17:50:15: 24000000 INFO @ Sat, 15 Jan 2022 17:50:23: 24000000 INFO @ Sat, 15 Jan 2022 17:50:26: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:50:26: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:50:26: #1 total tags in treatment: 24960750 INFO @ Sat, 15 Jan 2022 17:50:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:50:26: #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 17:50:27: #1 tags after filtering in treatment: 24960639 INFO @ Sat, 15 Jan 2022 17:50:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:50:27: #1 finished! INFO @ Sat, 15 Jan 2022 17:50:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:50:30: #2 number of paired peaks: 6992 INFO @ Sat, 15 Jan 2022 17:50:30: start model_add_line... INFO @ Sat, 15 Jan 2022 17:50:30: start X-correlation... INFO @ Sat, 15 Jan 2022 17:50:30: end of X-cor INFO @ Sat, 15 Jan 2022 17:50:30: #2 finished! INFO @ Sat, 15 Jan 2022 17:50:30: #2 predicted fragment length is 79 bps INFO @ Sat, 15 Jan 2022 17:50:30: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 15 Jan 2022 17:50:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.05_model.r WARNING @ Sat, 15 Jan 2022 17:50:30: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:50:30: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Sat, 15 Jan 2022 17:50:30: #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 17:50:30: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:50:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:50:33: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:50:33: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:50:33: #1 total tags in treatment: 24960750 INFO @ Sat, 15 Jan 2022 17:50:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:50:33: #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 17:50:34: #1 tags after filtering in treatment: 24960639 INFO @ Sat, 15 Jan 2022 17:50:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:50:34: #1 finished! INFO @ Sat, 15 Jan 2022 17:50:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:50:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:50:37: #2 number of paired peaks: 6992 INFO @ Sat, 15 Jan 2022 17:50:37: start model_add_line... INFO @ Sat, 15 Jan 2022 17:50:37: start X-correlation... INFO @ Sat, 15 Jan 2022 17:50:37: end of X-cor INFO @ Sat, 15 Jan 2022 17:50:37: #2 finished! INFO @ Sat, 15 Jan 2022 17:50:37: #2 predicted fragment length is 79 bps INFO @ Sat, 15 Jan 2022 17:50:37: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 15 Jan 2022 17:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.20_model.r WARNING @ Sat, 15 Jan 2022 17:50:37: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:50:37: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Sat, 15 Jan 2022 17:50:37: #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 17:50:37: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:50:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:51:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:51:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:51:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:52:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:52:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:52:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.10_summits.bed INFO @ Sat, 15 Jan 2022 17:52:07: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (1211 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:52:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:52:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:52:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.05_summits.bed INFO @ Sat, 15 Jan 2022 17:52:34: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (2943 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:52:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:52:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:52:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963445/SRX9963445.20_summits.bed INFO @ Sat, 15 Jan 2022 17:52:40: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (488 records, 4 fields): 4 millis CompletedMACS2peakCalling