Job ID = 12531442 SRX = SRX3087667 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16285975 spots for SRR5927303/SRR5927303.sra Written 16285975 spots for SRR5927303/SRR5927303.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:02 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:27:32 16285975 reads; of these: 16285975 (100.00%) were unpaired; of these: 1151519 (7.07%) aligned 0 times 11047271 (67.83%) aligned exactly 1 time 4087185 (25.10%) aligned >1 times 92.93% overall alignment rate Time searching: 00:27:40 Overall time: 00:27:40 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] 1754058 / 15134456 = 0.1159 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:00:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.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, 17 Apr 2021 08:00:46: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:00:46: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:01:01: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:01:14: 2000000 INFO @ Sat, 17 Apr 2021 08:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.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, 17 Apr 2021 08:01:16: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:01:16: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:01:26: 1000000 INFO @ Sat, 17 Apr 2021 08:01:27: 3000000 INFO @ Sat, 17 Apr 2021 08:01:37: 2000000 INFO @ Sat, 17 Apr 2021 08:01:41: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.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, 17 Apr 2021 08:01:46: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:01:46: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:01:49: 3000000 INFO @ Sat, 17 Apr 2021 08:01:52: 5000000 INFO @ Sat, 17 Apr 2021 08:01:58: 1000000 INFO @ Sat, 17 Apr 2021 08:02:02: 4000000 INFO @ Sat, 17 Apr 2021 08:02:04: 6000000 INFO @ Sat, 17 Apr 2021 08:02:14: 2000000 INFO @ Sat, 17 Apr 2021 08:02:15: 7000000 INFO @ Sat, 17 Apr 2021 08:02:15: 5000000 INFO @ Sat, 17 Apr 2021 08:02:28: 8000000 INFO @ Sat, 17 Apr 2021 08:02:29: 3000000 INFO @ Sat, 17 Apr 2021 08:02:29: 6000000 INFO @ Sat, 17 Apr 2021 08:02:42: 4000000 INFO @ Sat, 17 Apr 2021 08:02:43: 7000000 INFO @ Sat, 17 Apr 2021 08:02:45: 9000000 INFO @ Sat, 17 Apr 2021 08:02:54: 8000000 INFO @ Sat, 17 Apr 2021 08:02:57: 5000000 INFO @ Sat, 17 Apr 2021 08:03:00: 10000000 INFO @ Sat, 17 Apr 2021 08:03:07: 9000000 INFO @ Sat, 17 Apr 2021 08:03:10: 6000000 INFO @ Sat, 17 Apr 2021 08:03:14: 11000000 INFO @ Sat, 17 Apr 2021 08:03:21: 10000000 INFO @ Sat, 17 Apr 2021 08:03:22: 7000000 INFO @ Sat, 17 Apr 2021 08:03:26: 12000000 INFO @ Sat, 17 Apr 2021 08:03:32: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:03:35: 8000000 INFO @ Sat, 17 Apr 2021 08:03:39: 13000000 INFO @ Sat, 17 Apr 2021 08:03:44: 12000000 INFO @ Sat, 17 Apr 2021 08:03:44: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:03:44: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:03:44: #1 total tags in treatment: 13380398 INFO @ Sat, 17 Apr 2021 08:03:44: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:03:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:03:44: #1 tags after filtering in treatment: 13380213 INFO @ Sat, 17 Apr 2021 08:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:03:44: #1 finished! INFO @ Sat, 17 Apr 2021 08:03:44: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:03:47: #2 number of paired peaks: 16652 INFO @ Sat, 17 Apr 2021 08:03:47: start model_add_line... INFO @ Sat, 17 Apr 2021 08:03:47: start X-correlation... INFO @ Sat, 17 Apr 2021 08:03:47: end of X-cor INFO @ Sat, 17 Apr 2021 08:03:47: #2 finished! INFO @ Sat, 17 Apr 2021 08:03:47: #2 predicted fragment length is 86 bps INFO @ Sat, 17 Apr 2021 08:03:47: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 17 Apr 2021 08:03:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.05_model.r WARNING @ Sat, 17 Apr 2021 08:03:47: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:03:47: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 17 Apr 2021 08:03:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:03:47: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:03:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:03:47: 9000000 INFO @ Sat, 17 Apr 2021 08:03:57: 13000000 INFO @ Sat, 17 Apr 2021 08:04:01: 10000000 INFO @ Sat, 17 Apr 2021 08:04:02: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:04:02: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:04:02: #1 total tags in treatment: 13380398 INFO @ Sat, 17 Apr 2021 08:04:02: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:04:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:04:03: #1 tags after filtering in treatment: 13380213 INFO @ Sat, 17 Apr 2021 08:04:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:04:03: #1 finished! INFO @ Sat, 17 Apr 2021 08:04:03: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:04:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:04:05: #2 number of paired peaks: 16652 INFO @ Sat, 17 Apr 2021 08:04:05: start model_add_line... INFO @ Sat, 17 Apr 2021 08:04:05: start X-correlation... INFO @ Sat, 17 Apr 2021 08:04:05: end of X-cor INFO @ Sat, 17 Apr 2021 08:04:05: #2 finished! INFO @ Sat, 17 Apr 2021 08:04:05: #2 predicted fragment length is 86 bps INFO @ Sat, 17 Apr 2021 08:04:05: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 17 Apr 2021 08:04:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.10_model.r WARNING @ Sat, 17 Apr 2021 08:04:05: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:04:05: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 17 Apr 2021 08:04:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:04:05: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:04:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:04:13: 11000000 INFO @ Sat, 17 Apr 2021 08:04:23: 12000000 INFO @ Sat, 17 Apr 2021 08:04:26: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:04:34: 13000000 INFO @ Sat, 17 Apr 2021 08:04:38: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:04:38: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:04:38: #1 total tags in treatment: 13380398 INFO @ Sat, 17 Apr 2021 08:04:38: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:04:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:04:38: #1 tags after filtering in treatment: 13380213 INFO @ Sat, 17 Apr 2021 08:04:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:04:38: #1 finished! INFO @ Sat, 17 Apr 2021 08:04:38: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:04:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:04:40: #2 number of paired peaks: 16652 INFO @ Sat, 17 Apr 2021 08:04:40: start model_add_line... INFO @ Sat, 17 Apr 2021 08:04:40: start X-correlation... INFO @ Sat, 17 Apr 2021 08:04:40: end of X-cor INFO @ Sat, 17 Apr 2021 08:04:40: #2 finished! INFO @ Sat, 17 Apr 2021 08:04:40: #2 predicted fragment length is 86 bps INFO @ Sat, 17 Apr 2021 08:04:40: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 17 Apr 2021 08:04:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.20_model.r WARNING @ Sat, 17 Apr 2021 08:04:41: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:04:41: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 17 Apr 2021 08:04:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:04:41: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:04:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:04:45: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:04:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:04:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:04:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.05_summits.bed INFO @ Sat, 17 Apr 2021 08:04:47: Done! pass1 - making usageList (48 chroms): 4 millis pass2 - checking and writing primary data (4162 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:05:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:05:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:05:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.10_summits.bed INFO @ Sat, 17 Apr 2021 08:05:06: Done! pass1 - making usageList (32 chroms): 4 millis pass2 - checking and writing primary data (1148 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:05:20: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:05:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:05:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:05:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087667/SRX3087667.20_summits.bed INFO @ Sat, 17 Apr 2021 08:05:40: Done! pass1 - making usageList (27 chroms): 10 millis pass2 - checking and writing primary data (201 records, 4 fields): 16 millis CompletedMACS2peakCalling