Job ID = 14519485 SRX = SRX9963504 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 41363623 spots for SRR13565218/SRR13565218.sra Written 41363623 spots for SRR13565218/SRR13565218.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: 00:00:00 Multiseed full-index search: 01:18:47 41363623 reads; of these: 41363623 (100.00%) were unpaired; of these: 7985082 (19.30%) aligned 0 times 16063815 (38.84%) aligned exactly 1 time 17314726 (41.86%) aligned >1 times 80.70% overall alignment rate Time searching: 01:18:50 Overall time: 01:18:50 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] 8678937 / 33378541 = 0.2600 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 16:30:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.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 16:30:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 16:30:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 16:30:55: 1000000 INFO @ Sat, 15 Jan 2022 16:31:08: 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 16:31:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.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 16:31:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 16:31:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 16:31:19: 3000000 INFO @ Sat, 15 Jan 2022 16:31:24: 1000000 INFO @ Sat, 15 Jan 2022 16:31:31: 4000000 INFO @ Sat, 15 Jan 2022 16:31:34: 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 16:31:43: 5000000 INFO @ Sat, 15 Jan 2022 16:31:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.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 16:31:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 16:31:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 16:31:45: 3000000 INFO @ Sat, 15 Jan 2022 16:31:55: 4000000 INFO @ Sat, 15 Jan 2022 16:31:55: 6000000 INFO @ Sat, 15 Jan 2022 16:31:56: 1000000 INFO @ Sat, 15 Jan 2022 16:32:05: 5000000 INFO @ Sat, 15 Jan 2022 16:32:08: 7000000 INFO @ Sat, 15 Jan 2022 16:32:09: 2000000 INFO @ Sat, 15 Jan 2022 16:32:15: 6000000 INFO @ Sat, 15 Jan 2022 16:32:20: 8000000 INFO @ Sat, 15 Jan 2022 16:32:22: 3000000 INFO @ Sat, 15 Jan 2022 16:32:25: 7000000 INFO @ Sat, 15 Jan 2022 16:32:33: 9000000 INFO @ Sat, 15 Jan 2022 16:32:34: 4000000 INFO @ Sat, 15 Jan 2022 16:32:35: 8000000 INFO @ Sat, 15 Jan 2022 16:32:45: 9000000 INFO @ Sat, 15 Jan 2022 16:32:46: 10000000 INFO @ Sat, 15 Jan 2022 16:32:47: 5000000 INFO @ Sat, 15 Jan 2022 16:32:56: 10000000 INFO @ Sat, 15 Jan 2022 16:32:58: 11000000 INFO @ Sat, 15 Jan 2022 16:33:00: 6000000 INFO @ Sat, 15 Jan 2022 16:33:06: 11000000 INFO @ Sat, 15 Jan 2022 16:33:11: 12000000 INFO @ Sat, 15 Jan 2022 16:33:13: 7000000 INFO @ Sat, 15 Jan 2022 16:33:16: 12000000 INFO @ Sat, 15 Jan 2022 16:33:24: 13000000 INFO @ Sat, 15 Jan 2022 16:33:26: 8000000 INFO @ Sat, 15 Jan 2022 16:33:27: 13000000 INFO @ Sat, 15 Jan 2022 16:33:36: 14000000 INFO @ Sat, 15 Jan 2022 16:33:37: 14000000 INFO @ Sat, 15 Jan 2022 16:33:39: 9000000 INFO @ Sat, 15 Jan 2022 16:33:47: 15000000 INFO @ Sat, 15 Jan 2022 16:33:49: 15000000 INFO @ Sat, 15 Jan 2022 16:33:52: 10000000 INFO @ Sat, 15 Jan 2022 16:33:57: 16000000 INFO @ Sat, 15 Jan 2022 16:34:01: 16000000 INFO @ Sat, 15 Jan 2022 16:34:05: 11000000 INFO @ Sat, 15 Jan 2022 16:34:07: 17000000 INFO @ Sat, 15 Jan 2022 16:34:14: 17000000 INFO @ Sat, 15 Jan 2022 16:34:17: 18000000 INFO @ Sat, 15 Jan 2022 16:34:18: 12000000 INFO @ Sat, 15 Jan 2022 16:34:26: 18000000 INFO @ Sat, 15 Jan 2022 16:34:27: 19000000 INFO @ Sat, 15 Jan 2022 16:34:31: 13000000 INFO @ Sat, 15 Jan 2022 16:34:37: 19000000 INFO @ Sat, 15 Jan 2022 16:34:37: 20000000 INFO @ Sat, 15 Jan 2022 16:34:44: 14000000 INFO @ Sat, 15 Jan 2022 16:34:47: 21000000 INFO @ Sat, 15 Jan 2022 16:34:49: 20000000 INFO @ Sat, 15 Jan 2022 16:34:57: 15000000 INFO @ Sat, 15 Jan 2022 16:34:57: 22000000 INFO @ Sat, 15 Jan 2022 16:35:00: 21000000 INFO @ Sat, 15 Jan 2022 16:35:08: 23000000 INFO @ Sat, 15 Jan 2022 16:35:10: 16000000 INFO @ Sat, 15 Jan 2022 16:35:12: 22000000 INFO @ Sat, 15 Jan 2022 16:35:17: 24000000 INFO @ Sat, 15 Jan 2022 16:35:23: 17000000 INFO @ Sat, 15 Jan 2022 16:35:24: 23000000 INFO @ Sat, 15 Jan 2022 16:35:25: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 16:35:25: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 16:35:25: #1 total tags in treatment: 24699604 INFO @ Sat, 15 Jan 2022 16:35:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 16:35:25: #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 16:35:25: #1 tags after filtering in treatment: 24699502 INFO @ Sat, 15 Jan 2022 16:35:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 16:35:25: #1 finished! INFO @ Sat, 15 Jan 2022 16:35:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 16:35:25: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 16:35:31: #2 number of paired peaks: 69625 INFO @ Sat, 15 Jan 2022 16:35:31: start model_add_line... INFO @ Sat, 15 Jan 2022 16:35:32: start X-correlation... INFO @ Sat, 15 Jan 2022 16:35:32: end of X-cor INFO @ Sat, 15 Jan 2022 16:35:32: #2 finished! INFO @ Sat, 15 Jan 2022 16:35:32: #2 predicted fragment length is 89 bps INFO @ Sat, 15 Jan 2022 16:35:32: #2 alternative fragment length(s) may be 89 bps INFO @ Sat, 15 Jan 2022 16:35:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.10_model.r WARNING @ Sat, 15 Jan 2022 16:35:32: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 16:35:32: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Sat, 15 Jan 2022 16:35:32: #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 16:35:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 16:35:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 16:35:35: 18000000 INFO @ Sat, 15 Jan 2022 16:35:36: 24000000 INFO @ Sat, 15 Jan 2022 16:35:44: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 16:35:44: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 16:35:44: #1 total tags in treatment: 24699604 INFO @ Sat, 15 Jan 2022 16:35:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 16:35:44: #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 16:35:45: #1 tags after filtering in treatment: 24699502 INFO @ Sat, 15 Jan 2022 16:35:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 16:35:45: #1 finished! INFO @ Sat, 15 Jan 2022 16:35:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 16:35:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 16:35:48: 19000000 INFO @ Sat, 15 Jan 2022 16:35:51: #2 number of paired peaks: 69625 INFO @ Sat, 15 Jan 2022 16:35:51: start model_add_line... INFO @ Sat, 15 Jan 2022 16:35:51: start X-correlation... INFO @ Sat, 15 Jan 2022 16:35:51: end of X-cor INFO @ Sat, 15 Jan 2022 16:35:51: #2 finished! INFO @ Sat, 15 Jan 2022 16:35:51: #2 predicted fragment length is 89 bps INFO @ Sat, 15 Jan 2022 16:35:51: #2 alternative fragment length(s) may be 89 bps INFO @ Sat, 15 Jan 2022 16:35:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.05_model.r WARNING @ Sat, 15 Jan 2022 16:35:51: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 16:35:51: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Sat, 15 Jan 2022 16:35:51: #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 16:35:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 16:35:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 16:36:00: 20000000 INFO @ Sat, 15 Jan 2022 16:36:12: 21000000 INFO @ Sat, 15 Jan 2022 16:36:24: 22000000 INFO @ Sat, 15 Jan 2022 16:36:37: 23000000 INFO @ Sat, 15 Jan 2022 16:36:49: 24000000 INFO @ Sat, 15 Jan 2022 16:36:57: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 16:36:57: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 16:36:57: #1 total tags in treatment: 24699604 INFO @ Sat, 15 Jan 2022 16:36:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 16:36:57: #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 16:36:58: #1 tags after filtering in treatment: 24699502 INFO @ Sat, 15 Jan 2022 16:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 16:36:58: #1 finished! INFO @ Sat, 15 Jan 2022 16:36:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 16:36:58: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 16:37:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 16:37:04: #2 number of paired peaks: 69625 INFO @ Sat, 15 Jan 2022 16:37:04: start model_add_line... INFO @ Sat, 15 Jan 2022 16:37:04: start X-correlation... INFO @ Sat, 15 Jan 2022 16:37:04: end of X-cor INFO @ Sat, 15 Jan 2022 16:37:04: #2 finished! INFO @ Sat, 15 Jan 2022 16:37:04: #2 predicted fragment length is 89 bps INFO @ Sat, 15 Jan 2022 16:37:04: #2 alternative fragment length(s) may be 89 bps INFO @ Sat, 15 Jan 2022 16:37:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.20_model.r WARNING @ Sat, 15 Jan 2022 16:37:04: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 16:37:04: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Sat, 15 Jan 2022 16:37:04: #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 16:37:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 16:37:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 16:37:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 16:37:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.10_peaks.xls INFO @ Sat, 15 Jan 2022 16:37:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 16:37:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.10_summits.bed INFO @ Sat, 15 Jan 2022 16:37:48: Done! pass1 - making usageList (132 chroms): 3 millis pass2 - checking and writing primary data (6537 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 16:38:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.05_peaks.xls INFO @ Sat, 15 Jan 2022 16:38:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 16:38:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.05_summits.bed INFO @ Sat, 15 Jan 2022 16:38:07: Done! pass1 - making usageList (212 chroms): 5 millis pass2 - checking and writing primary data (21588 records, 4 fields): 341 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 16:38:33: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 16:39:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.20_peaks.xls INFO @ Sat, 15 Jan 2022 16:39:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 16:39:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963504/SRX9963504.20_summits.bed INFO @ Sat, 15 Jan 2022 16:39:18: Done! pass1 - making usageList (65 chroms): 3 millis pass2 - checking and writing primary data (1862 records, 4 fields): 11 millis CompletedMACS2peakCalling