Job ID = 14519646 SRX = SRX6581749 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 28536050 spots for SRR9825082/SRR9825082.sra Written 28536050 spots for SRR9825082/SRR9825082.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:50:38 28536050 reads; of these: 28536050 (100.00%) were unpaired; of these: 749165 (2.63%) aligned 0 times 20650966 (72.37%) aligned exactly 1 time 7135919 (25.01%) aligned >1 times 97.37% overall alignment rate Time searching: 00:50:41 Overall time: 00:50:41 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] 5752744 / 27786885 = 0.2070 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 18:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.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 18:14:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:14:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:14:24: 1000000 INFO @ Sat, 15 Jan 2022 18:14:32: 2000000 INFO @ Sat, 15 Jan 2022 18:14:41: 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 18:14:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.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 18:14:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:14:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:14:49: 4000000 INFO @ Sat, 15 Jan 2022 18:14:54: 1000000 INFO @ Sat, 15 Jan 2022 18:14:58: 5000000 INFO @ Sat, 15 Jan 2022 18:15:05: 2000000 INFO @ Sat, 15 Jan 2022 18:15:07: 6000000 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 18:15:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.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 18:15:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:15:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:15:16: 3000000 INFO @ Sat, 15 Jan 2022 18:15:16: 7000000 INFO @ Sat, 15 Jan 2022 18:15:24: 1000000 INFO @ Sat, 15 Jan 2022 18:15:25: 8000000 INFO @ Sat, 15 Jan 2022 18:15:26: 4000000 INFO @ Sat, 15 Jan 2022 18:15:33: 9000000 INFO @ Sat, 15 Jan 2022 18:15:34: 2000000 INFO @ Sat, 15 Jan 2022 18:15:37: 5000000 INFO @ Sat, 15 Jan 2022 18:15:42: 10000000 INFO @ Sat, 15 Jan 2022 18:15:43: 3000000 INFO @ Sat, 15 Jan 2022 18:15:47: 6000000 INFO @ Sat, 15 Jan 2022 18:15:51: 11000000 INFO @ Sat, 15 Jan 2022 18:15:54: 4000000 INFO @ Sat, 15 Jan 2022 18:15:58: 7000000 INFO @ Sat, 15 Jan 2022 18:16:00: 12000000 INFO @ Sat, 15 Jan 2022 18:16:04: 5000000 INFO @ Sat, 15 Jan 2022 18:16:08: 8000000 INFO @ Sat, 15 Jan 2022 18:16:09: 13000000 INFO @ Sat, 15 Jan 2022 18:16:15: 6000000 INFO @ Sat, 15 Jan 2022 18:16:17: 14000000 INFO @ Sat, 15 Jan 2022 18:16:19: 9000000 INFO @ Sat, 15 Jan 2022 18:16:25: 7000000 INFO @ Sat, 15 Jan 2022 18:16:26: 15000000 INFO @ Sat, 15 Jan 2022 18:16:30: 10000000 INFO @ Sat, 15 Jan 2022 18:16:35: 16000000 INFO @ Sat, 15 Jan 2022 18:16:36: 8000000 INFO @ Sat, 15 Jan 2022 18:16:41: 11000000 INFO @ Sat, 15 Jan 2022 18:16:44: 17000000 INFO @ Sat, 15 Jan 2022 18:16:46: 9000000 INFO @ Sat, 15 Jan 2022 18:16:51: 12000000 INFO @ Sat, 15 Jan 2022 18:16:53: 18000000 INFO @ Sat, 15 Jan 2022 18:16:56: 10000000 INFO @ Sat, 15 Jan 2022 18:17:01: 19000000 INFO @ Sat, 15 Jan 2022 18:17:02: 13000000 INFO @ Sat, 15 Jan 2022 18:17:05: 11000000 INFO @ Sat, 15 Jan 2022 18:17:10: 20000000 INFO @ Sat, 15 Jan 2022 18:17:13: 14000000 INFO @ Sat, 15 Jan 2022 18:17:15: 12000000 INFO @ Sat, 15 Jan 2022 18:17:19: 21000000 INFO @ Sat, 15 Jan 2022 18:17:24: 15000000 INFO @ Sat, 15 Jan 2022 18:17:25: 13000000 INFO @ Sat, 15 Jan 2022 18:17:28: 22000000 INFO @ Sat, 15 Jan 2022 18:17:29: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 18:17:29: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 18:17:29: #1 total tags in treatment: 22034141 INFO @ Sat, 15 Jan 2022 18:17:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:17:29: #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 18:17:29: #1 tags after filtering in treatment: 22034012 INFO @ Sat, 15 Jan 2022 18:17:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 18:17:29: #1 finished! INFO @ Sat, 15 Jan 2022 18:17:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:17:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:17:32: #2 number of paired peaks: 10243 INFO @ Sat, 15 Jan 2022 18:17:32: start model_add_line... INFO @ Sat, 15 Jan 2022 18:17:32: start X-correlation... INFO @ Sat, 15 Jan 2022 18:17:32: end of X-cor INFO @ Sat, 15 Jan 2022 18:17:32: #2 finished! INFO @ Sat, 15 Jan 2022 18:17:32: #2 predicted fragment length is 146 bps INFO @ Sat, 15 Jan 2022 18:17:32: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 15 Jan 2022 18:17:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.05_model.r WARNING @ Sat, 15 Jan 2022 18:17:32: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:17:32: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sat, 15 Jan 2022 18:17:32: #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 18:17:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:17:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:17:35: 16000000 INFO @ Sat, 15 Jan 2022 18:17:35: 14000000 INFO @ Sat, 15 Jan 2022 18:17:45: 15000000 INFO @ Sat, 15 Jan 2022 18:17:46: 17000000 INFO @ Sat, 15 Jan 2022 18:17:55: 16000000 INFO @ Sat, 15 Jan 2022 18:17:57: 18000000 INFO @ Sat, 15 Jan 2022 18:18:05: 17000000 INFO @ Sat, 15 Jan 2022 18:18:08: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:18:15: 18000000 INFO @ Sat, 15 Jan 2022 18:18:19: 20000000 INFO @ Sat, 15 Jan 2022 18:18:24: 19000000 INFO @ Sat, 15 Jan 2022 18:18:30: 21000000 INFO @ Sat, 15 Jan 2022 18:18:34: 20000000 INFO @ Sat, 15 Jan 2022 18:18:41: 22000000 INFO @ Sat, 15 Jan 2022 18:18:42: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 18:18:42: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 18:18:42: #1 total tags in treatment: 22034141 INFO @ Sat, 15 Jan 2022 18:18:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:18:42: #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 18:18:42: #1 tags after filtering in treatment: 22034012 INFO @ Sat, 15 Jan 2022 18:18:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 18:18:42: #1 finished! INFO @ Sat, 15 Jan 2022 18:18:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:18:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:18:44: 21000000 INFO @ Sat, 15 Jan 2022 18:18:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:18:45: #2 number of paired peaks: 10243 INFO @ Sat, 15 Jan 2022 18:18:45: start model_add_line... INFO @ Sat, 15 Jan 2022 18:18:45: start X-correlation... INFO @ Sat, 15 Jan 2022 18:18:45: end of X-cor INFO @ Sat, 15 Jan 2022 18:18:45: #2 finished! INFO @ Sat, 15 Jan 2022 18:18:45: #2 predicted fragment length is 146 bps INFO @ Sat, 15 Jan 2022 18:18:45: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 15 Jan 2022 18:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.10_model.r WARNING @ Sat, 15 Jan 2022 18:18:45: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:18:45: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sat, 15 Jan 2022 18:18:45: #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 18:18:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:18:54: 22000000 INFO @ Sat, 15 Jan 2022 18:18:54: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 18:18:54: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 18:18:54: #1 total tags in treatment: 22034141 INFO @ Sat, 15 Jan 2022 18:18:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:18:54: #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 18:18:55: #1 tags after filtering in treatment: 22034012 INFO @ Sat, 15 Jan 2022 18:18:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 18:18:55: #1 finished! INFO @ Sat, 15 Jan 2022 18:18:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:18:57: #2 number of paired peaks: 10243 INFO @ Sat, 15 Jan 2022 18:18:57: start model_add_line... INFO @ Sat, 15 Jan 2022 18:18:58: start X-correlation... INFO @ Sat, 15 Jan 2022 18:18:58: end of X-cor INFO @ Sat, 15 Jan 2022 18:18:58: #2 finished! INFO @ Sat, 15 Jan 2022 18:18:58: #2 predicted fragment length is 146 bps INFO @ Sat, 15 Jan 2022 18:18:58: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 15 Jan 2022 18:18:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.20_model.r WARNING @ Sat, 15 Jan 2022 18:18:58: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:18:58: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sat, 15 Jan 2022 18:18:58: #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 18:18:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:18:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:19:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:19:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:19:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.05_summits.bed INFO @ Sat, 15 Jan 2022 18:19:19: Done! pass1 - making usageList (63 chroms): 2 millis pass2 - checking and writing primary data (5913 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:19:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:20:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:20:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:20:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:20:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.10_summits.bed INFO @ Sat, 15 Jan 2022 18:20:30: Done! pass1 - making usageList (49 chroms): 2 millis pass2 - checking and writing primary data (2941 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581749/SRX6581749.20_summits.bed INFO @ Sat, 15 Jan 2022 18:20:44: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (1185 records, 4 fields): 5 millis CompletedMACS2peakCalling