Job ID = 12531444 SRX = SRX3087669 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22404837 spots for SRR5927305/SRR5927305.sra Written 22404837 spots for SRR5927305/SRR5927305.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:24:43 22404837 reads; of these: 22404837 (100.00%) were unpaired; of these: 2829796 (12.63%) aligned 0 times 14924033 (66.61%) aligned exactly 1 time 4651008 (20.76%) aligned >1 times 87.37% overall alignment rate Time searching: 00:24:48 Overall time: 00:24:48 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] 2445249 / 19575041 = 0.1249 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 07:57:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.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 07:57:54: #1 read tag files... INFO @ Sat, 17 Apr 2021 07:57:54: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 07:58:01: 1000000 INFO @ Sat, 17 Apr 2021 07:58:08: 2000000 INFO @ Sat, 17 Apr 2021 07:58:15: 3000000 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 07:58:22: 4000000 INFO @ Sat, 17 Apr 2021 07:58:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.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 07:58:24: #1 read tag files... INFO @ Sat, 17 Apr 2021 07:58:24: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 07:58:30: 5000000 INFO @ Sat, 17 Apr 2021 07:58:31: 1000000 INFO @ Sat, 17 Apr 2021 07:58:37: 6000000 INFO @ Sat, 17 Apr 2021 07:58:39: 2000000 INFO @ Sat, 17 Apr 2021 07:58:45: 7000000 INFO @ Sat, 17 Apr 2021 07:58:46: 3000000 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 07:58:53: 8000000 INFO @ Sat, 17 Apr 2021 07:58:53: 4000000 INFO @ Sat, 17 Apr 2021 07:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.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 07:58:54: #1 read tag files... INFO @ Sat, 17 Apr 2021 07:58:54: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 07:59:01: 9000000 INFO @ Sat, 17 Apr 2021 07:59:01: 5000000 INFO @ Sat, 17 Apr 2021 07:59:01: 1000000 INFO @ Sat, 17 Apr 2021 07:59:08: 6000000 INFO @ Sat, 17 Apr 2021 07:59:09: 10000000 INFO @ Sat, 17 Apr 2021 07:59:09: 2000000 INFO @ Sat, 17 Apr 2021 07:59:16: 7000000 INFO @ Sat, 17 Apr 2021 07:59:16: 3000000 INFO @ Sat, 17 Apr 2021 07:59:17: 11000000 INFO @ Sat, 17 Apr 2021 07:59:23: 8000000 INFO @ Sat, 17 Apr 2021 07:59:24: 4000000 INFO @ Sat, 17 Apr 2021 07:59:25: 12000000 INFO @ Sat, 17 Apr 2021 07:59:31: 9000000 INFO @ Sat, 17 Apr 2021 07:59:31: 5000000 INFO @ Sat, 17 Apr 2021 07:59:33: 13000000 INFO @ Sat, 17 Apr 2021 07:59:38: 10000000 INFO @ Sat, 17 Apr 2021 07:59:39: 6000000 INFO @ Sat, 17 Apr 2021 07:59:41: 14000000 INFO @ Sat, 17 Apr 2021 07:59:46: 11000000 INFO @ Sat, 17 Apr 2021 07:59:47: 7000000 INFO @ Sat, 17 Apr 2021 07:59:49: 15000000 INFO @ Sat, 17 Apr 2021 07:59:53: 12000000 INFO @ Sat, 17 Apr 2021 07:59:54: 8000000 INFO @ Sat, 17 Apr 2021 07:59:57: 16000000 INFO @ Sat, 17 Apr 2021 08:00:01: 13000000 INFO @ Sat, 17 Apr 2021 08:00:02: 9000000 INFO @ Sat, 17 Apr 2021 08:00:05: 17000000 INFO @ Sat, 17 Apr 2021 08:00:06: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:00:06: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:00:06: #1 total tags in treatment: 17129792 INFO @ Sat, 17 Apr 2021 08:00:06: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:00:06: #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 08:00:07: #1 tags after filtering in treatment: 17129618 INFO @ Sat, 17 Apr 2021 08:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:00:07: #1 finished! INFO @ Sat, 17 Apr 2021 08:00:07: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:00:08: 14000000 INFO @ Sat, 17 Apr 2021 08:00:09: 10000000 INFO @ Sat, 17 Apr 2021 08:00:09: #2 number of paired peaks: 35647 INFO @ Sat, 17 Apr 2021 08:00:09: start model_add_line... INFO @ Sat, 17 Apr 2021 08:00:09: start X-correlation... INFO @ Sat, 17 Apr 2021 08:00:09: end of X-cor INFO @ Sat, 17 Apr 2021 08:00:09: #2 finished! INFO @ Sat, 17 Apr 2021 08:00:09: #2 predicted fragment length is 114 bps INFO @ Sat, 17 Apr 2021 08:00:09: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 17 Apr 2021 08:00:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.05_model.r WARNING @ Sat, 17 Apr 2021 08:00:09: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:00:09: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sat, 17 Apr 2021 08:00:09: #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 08:00:09: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:00:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:00:15: 15000000 INFO @ Sat, 17 Apr 2021 08:00:16: 11000000 INFO @ Sat, 17 Apr 2021 08:00:23: 16000000 INFO @ Sat, 17 Apr 2021 08:00:23: 12000000 INFO @ Sat, 17 Apr 2021 08:00:30: 17000000 INFO @ Sat, 17 Apr 2021 08:00:30: 13000000 INFO @ Sat, 17 Apr 2021 08:00:31: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:00:31: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:00:31: #1 total tags in treatment: 17129792 INFO @ Sat, 17 Apr 2021 08:00:31: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:00:31: #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 08:00:31: #1 tags after filtering in treatment: 17129618 INFO @ Sat, 17 Apr 2021 08:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:00:31: #1 finished! INFO @ Sat, 17 Apr 2021 08:00:31: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:00:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:00:34: #2 number of paired peaks: 35647 INFO @ Sat, 17 Apr 2021 08:00:34: start model_add_line... INFO @ Sat, 17 Apr 2021 08:00:34: start X-correlation... INFO @ Sat, 17 Apr 2021 08:00:34: end of X-cor INFO @ Sat, 17 Apr 2021 08:00:34: #2 finished! INFO @ Sat, 17 Apr 2021 08:00:34: #2 predicted fragment length is 114 bps INFO @ Sat, 17 Apr 2021 08:00:34: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 17 Apr 2021 08:00:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.10_model.r WARNING @ Sat, 17 Apr 2021 08:00:34: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:00:34: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sat, 17 Apr 2021 08:00:34: #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 08:00:34: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:00:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:00:37: 14000000 INFO @ Sat, 17 Apr 2021 08:00:43: 15000000 INFO @ Sat, 17 Apr 2021 08:00:49: 16000000 INFO @ Sat, 17 Apr 2021 08:00:53: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:00:56: 17000000 INFO @ Sat, 17 Apr 2021 08:00:57: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:00:57: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:00:57: #1 total tags in treatment: 17129792 INFO @ Sat, 17 Apr 2021 08:00:57: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:00:57: #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 08:00:57: #1 tags after filtering in treatment: 17129618 INFO @ Sat, 17 Apr 2021 08:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:00:57: #1 finished! INFO @ Sat, 17 Apr 2021 08:00:57: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:01:00: #2 number of paired peaks: 35647 INFO @ Sat, 17 Apr 2021 08:01:00: start model_add_line... INFO @ Sat, 17 Apr 2021 08:01:00: start X-correlation... INFO @ Sat, 17 Apr 2021 08:01:00: end of X-cor INFO @ Sat, 17 Apr 2021 08:01:00: #2 finished! INFO @ Sat, 17 Apr 2021 08:01:00: #2 predicted fragment length is 114 bps INFO @ Sat, 17 Apr 2021 08:01:00: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 17 Apr 2021 08:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.20_model.r WARNING @ Sat, 17 Apr 2021 08:01:00: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:01:00: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sat, 17 Apr 2021 08:01:00: #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 08:01:00: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:01:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:01:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:01:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.05_summits.bed INFO @ Sat, 17 Apr 2021 08:01:15: Done! pass1 - making usageList (88 chroms): 4 millis pass2 - checking and writing primary data (20162 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:01:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:01:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:01:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:01:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.10_summits.bed INFO @ Sat, 17 Apr 2021 08:01:42: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (8798 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:01:45: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:02:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:02:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:02:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087669/SRX3087669.20_summits.bed INFO @ Sat, 17 Apr 2021 08:02:08: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (2229 records, 4 fields): 4 millis CompletedMACS2peakCalling