Job ID = 14519601 SRX = SRX6581713 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14320005 spots for SRR9825046/SRR9825046.sra Written 14320005 spots for SRR9825046/SRR9825046.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: 00:00:02 Multiseed full-index search: 00:32:43 14320005 reads; of these: 14320005 (100.00%) were unpaired; of these: 489268 (3.42%) aligned 0 times 9954708 (69.52%) aligned exactly 1 time 3876029 (27.07%) aligned >1 times 96.58% overall alignment rate Time searching: 00:32:47 Overall time: 00:32:47 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 8 files... [bam_rmdupse_core] 928346 / 13830737 = 0.0671 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 17:14:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.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 17:14:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:14:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:15:03: 1000000 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 17:15:18: 2000000 INFO @ Sat, 15 Jan 2022 17:15:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.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 17:15:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:15:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:15:31: 1000000 INFO @ Sat, 15 Jan 2022 17:15:33: 3000000 INFO @ Sat, 15 Jan 2022 17:15:43: 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 17:15:48: 4000000 INFO @ Sat, 15 Jan 2022 17:15:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.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 17:15:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:15:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:15:56: 3000000 INFO @ Sat, 15 Jan 2022 17:16:03: 5000000 INFO @ Sat, 15 Jan 2022 17:16:04: 1000000 INFO @ Sat, 15 Jan 2022 17:16:09: 4000000 INFO @ Sat, 15 Jan 2022 17:16:18: 6000000 INFO @ Sat, 15 Jan 2022 17:16:19: 2000000 INFO @ Sat, 15 Jan 2022 17:16:20: 5000000 INFO @ Sat, 15 Jan 2022 17:16:32: 7000000 INFO @ Sat, 15 Jan 2022 17:16:32: 6000000 INFO @ Sat, 15 Jan 2022 17:16:34: 3000000 INFO @ Sat, 15 Jan 2022 17:16:44: 7000000 INFO @ Sat, 15 Jan 2022 17:16:46: 8000000 INFO @ Sat, 15 Jan 2022 17:16:48: 4000000 INFO @ Sat, 15 Jan 2022 17:16:57: 8000000 INFO @ Sat, 15 Jan 2022 17:17:00: 9000000 INFO @ Sat, 15 Jan 2022 17:17:03: 5000000 INFO @ Sat, 15 Jan 2022 17:17:09: 9000000 INFO @ Sat, 15 Jan 2022 17:17:14: 10000000 INFO @ Sat, 15 Jan 2022 17:17:18: 6000000 INFO @ Sat, 15 Jan 2022 17:17:21: 10000000 INFO @ Sat, 15 Jan 2022 17:17:28: 11000000 INFO @ Sat, 15 Jan 2022 17:17:31: 7000000 INFO @ Sat, 15 Jan 2022 17:17:33: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:17:43: 12000000 INFO @ Sat, 15 Jan 2022 17:17:44: 12000000 INFO @ Sat, 15 Jan 2022 17:17:45: 8000000 INFO @ Sat, 15 Jan 2022 17:17:55: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:17:55: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:17:55: #1 total tags in treatment: 12902391 INFO @ Sat, 15 Jan 2022 17:17:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:17:55: #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 17:17:56: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:17:56: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:17:56: #1 total tags in treatment: 12902391 INFO @ Sat, 15 Jan 2022 17:17:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:17:56: #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 17:17:56: #1 tags after filtering in treatment: 12902218 INFO @ Sat, 15 Jan 2022 17:17:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:17:56: #1 finished! INFO @ Sat, 15 Jan 2022 17:17:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:17:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:17:56: #1 tags after filtering in treatment: 12902218 INFO @ Sat, 15 Jan 2022 17:17:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:17:56: #1 finished! INFO @ Sat, 15 Jan 2022 17:17:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:17:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:17:58: #2 number of paired peaks: 5382 INFO @ Sat, 15 Jan 2022 17:17:58: start model_add_line... INFO @ Sat, 15 Jan 2022 17:17:58: #2 number of paired peaks: 5382 INFO @ Sat, 15 Jan 2022 17:17:58: start model_add_line... INFO @ Sat, 15 Jan 2022 17:17:58: start X-correlation... INFO @ Sat, 15 Jan 2022 17:17:58: end of X-cor INFO @ Sat, 15 Jan 2022 17:17:58: #2 finished! INFO @ Sat, 15 Jan 2022 17:17:58: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:17:58: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 17:17:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.05_model.r WARNING @ Sat, 15 Jan 2022 17:17:58: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:17:58: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 17:17:58: #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 17:17:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:17:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:17:58: start X-correlation... INFO @ Sat, 15 Jan 2022 17:17:58: end of X-cor INFO @ Sat, 15 Jan 2022 17:17:58: #2 finished! INFO @ Sat, 15 Jan 2022 17:17:58: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:17:58: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 17:17:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.10_model.r WARNING @ Sat, 15 Jan 2022 17:17:58: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:17:58: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 17:17:58: #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 17:17:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:17:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:17:59: 9000000 INFO @ Sat, 15 Jan 2022 17:18:13: 10000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:18:26: 11000000 INFO @ Sat, 15 Jan 2022 17:18:40: 12000000 INFO @ Sat, 15 Jan 2022 17:18:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:18:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:18:52: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:18:52: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:18:52: #1 total tags in treatment: 12902391 INFO @ Sat, 15 Jan 2022 17:18:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:18:52: #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 17:18:52: #1 tags after filtering in treatment: 12902218 INFO @ Sat, 15 Jan 2022 17:18:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:18:52: #1 finished! INFO @ Sat, 15 Jan 2022 17:18:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:18:54: #2 number of paired peaks: 5382 INFO @ Sat, 15 Jan 2022 17:18:54: start model_add_line... INFO @ Sat, 15 Jan 2022 17:18:54: start X-correlation... INFO @ Sat, 15 Jan 2022 17:18:54: end of X-cor INFO @ Sat, 15 Jan 2022 17:18:54: #2 finished! INFO @ Sat, 15 Jan 2022 17:18:54: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:18:54: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 17:18:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.20_model.r WARNING @ Sat, 15 Jan 2022 17:18:54: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:18:54: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 17:18:54: #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 17:18:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:18:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:19:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:19:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:19:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.05_summits.bed INFO @ Sat, 15 Jan 2022 17:19:01: Done! INFO @ Sat, 15 Jan 2022 17:19:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:19:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:19:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.10_summits.bed INFO @ Sat, 15 Jan 2022 17:19:01: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (929 records, 4 fields): 16 millis CompletedMACS2peakCalling pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (576 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:19:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:19:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:19:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:19:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581713/SRX6581713.20_summits.bed INFO @ Sat, 15 Jan 2022 17:19:56: Done! pass1 - making usageList (25 chroms): 2 millis pass2 - checking and writing primary data (304 records, 4 fields): 3 millis CompletedMACS2peakCalling