Job ID = 8184233 SRX = SRX8047576 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:00:04 prefetch.2.10.7: 1) Downloading 'SRR11471301'... 2020-08-10T03:00:04 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:00:51 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:00:52 prefetch.2.10.7: 'SRR11471301' is valid 2020-08-10T03:00:52 prefetch.2.10.7: 1) 'SRR11471301' was downloaded successfully Read 11326572 spots for SRR11471301/SRR11471301.sra Written 11326572 spots for SRR11471301/SRR11471301.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: 00:00:01 Multiseed full-index search: 00:08:02 11326572 reads; of these: 11326572 (100.00%) were unpaired; of these: 390688 (3.45%) aligned 0 times 8134553 (71.82%) aligned exactly 1 time 2801331 (24.73%) aligned >1 times 96.55% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 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] 4023540 / 10935884 = 0.3679 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 10 Aug 2020 12:12:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.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 @ Mon, 10 Aug 2020 12:12:30: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:12:30: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:12:35: 1000000 INFO @ Mon, 10 Aug 2020 12:12:41: 2000000 INFO @ Mon, 10 Aug 2020 12:12:46: 3000000 INFO @ Mon, 10 Aug 2020 12:12:52: 4000000 INFO @ Mon, 10 Aug 2020 12:12:57: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 10 Aug 2020 12:13:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.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 @ Mon, 10 Aug 2020 12:13:00: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:13:00: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:13:03: 6000000 INFO @ Mon, 10 Aug 2020 12:13:05: 1000000 INFO @ Mon, 10 Aug 2020 12:13:08: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:13:08: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:13:08: #1 total tags in treatment: 6912344 INFO @ Mon, 10 Aug 2020 12:13:08: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:13:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 12:13:08: #1 tags after filtering in treatment: 6912127 INFO @ Mon, 10 Aug 2020 12:13:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:13:08: #1 finished! INFO @ Mon, 10 Aug 2020 12:13:08: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:13:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:13:09: #2 number of paired peaks: 11176 INFO @ Mon, 10 Aug 2020 12:13:09: start model_add_line... INFO @ Mon, 10 Aug 2020 12:13:09: start X-correlation... INFO @ Mon, 10 Aug 2020 12:13:09: end of X-cor INFO @ Mon, 10 Aug 2020 12:13:09: #2 finished! INFO @ Mon, 10 Aug 2020 12:13:09: #2 predicted fragment length is 53 bps INFO @ Mon, 10 Aug 2020 12:13:09: #2 alternative fragment length(s) may be 53,92 bps INFO @ Mon, 10 Aug 2020 12:13:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.05_model.r WARNING @ Mon, 10 Aug 2020 12:13:09: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 12:13:09: #2 You may need to consider one of the other alternative d(s): 53,92 WARNING @ Mon, 10 Aug 2020 12:13:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 12:13:09: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:13:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:13:10: 2000000 INFO @ Mon, 10 Aug 2020 12:13:15: 3000000 INFO @ Mon, 10 Aug 2020 12:13:20: 4000000 INFO @ Mon, 10 Aug 2020 12:13:25: 5000000 INFO @ Mon, 10 Aug 2020 12:13:25: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Mon, 10 Aug 2020 12:13:29: 6000000 INFO @ Mon, 10 Aug 2020 12:13:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.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 @ Mon, 10 Aug 2020 12:13:30: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:13:30: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:13:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.05_peaks.xls INFO @ Mon, 10 Aug 2020 12:13:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:13:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.05_summits.bed INFO @ Mon, 10 Aug 2020 12:13:33: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (767 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 12:13:34: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:13:34: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:13:34: #1 total tags in treatment: 6912344 INFO @ Mon, 10 Aug 2020 12:13:34: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:13:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 12:13:34: #1 tags after filtering in treatment: 6912127 INFO @ Mon, 10 Aug 2020 12:13:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:13:34: #1 finished! INFO @ Mon, 10 Aug 2020 12:13:34: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:13:35: 1000000 INFO @ Mon, 10 Aug 2020 12:13:36: #2 number of paired peaks: 11176 INFO @ Mon, 10 Aug 2020 12:13:36: start model_add_line... INFO @ Mon, 10 Aug 2020 12:13:36: start X-correlation... INFO @ Mon, 10 Aug 2020 12:13:36: end of X-cor INFO @ Mon, 10 Aug 2020 12:13:36: #2 finished! INFO @ Mon, 10 Aug 2020 12:13:36: #2 predicted fragment length is 53 bps INFO @ Mon, 10 Aug 2020 12:13:36: #2 alternative fragment length(s) may be 53,92 bps INFO @ Mon, 10 Aug 2020 12:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.10_model.r WARNING @ Mon, 10 Aug 2020 12:13:36: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 12:13:36: #2 You may need to consider one of the other alternative d(s): 53,92 WARNING @ Mon, 10 Aug 2020 12:13:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 12:13:36: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:13:40: 2000000 INFO @ Mon, 10 Aug 2020 12:13:45: 3000000 INFO @ Mon, 10 Aug 2020 12:13:50: 4000000 INFO @ Mon, 10 Aug 2020 12:13:51: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:13:55: 5000000 INFO @ Mon, 10 Aug 2020 12:13:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.10_peaks.xls INFO @ Mon, 10 Aug 2020 12:13:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:13:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.10_summits.bed INFO @ Mon, 10 Aug 2020 12:13:59: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (393 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 12:13:59: 6000000 INFO @ Mon, 10 Aug 2020 12:14:04: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:14:04: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:14:04: #1 total tags in treatment: 6912344 INFO @ Mon, 10 Aug 2020 12:14:04: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:14:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 12:14:04: #1 tags after filtering in treatment: 6912127 INFO @ Mon, 10 Aug 2020 12:14:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:14:04: #1 finished! INFO @ Mon, 10 Aug 2020 12:14:04: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:14:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:14:06: #2 number of paired peaks: 11176 INFO @ Mon, 10 Aug 2020 12:14:06: start model_add_line... INFO @ Mon, 10 Aug 2020 12:14:06: start X-correlation... INFO @ Mon, 10 Aug 2020 12:14:06: end of X-cor INFO @ Mon, 10 Aug 2020 12:14:06: #2 finished! INFO @ Mon, 10 Aug 2020 12:14:06: #2 predicted fragment length is 53 bps INFO @ Mon, 10 Aug 2020 12:14:06: #2 alternative fragment length(s) may be 53,92 bps INFO @ Mon, 10 Aug 2020 12:14:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.20_model.r WARNING @ Mon, 10 Aug 2020 12:14:06: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 12:14:06: #2 You may need to consider one of the other alternative d(s): 53,92 WARNING @ Mon, 10 Aug 2020 12:14:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 12:14:06: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:14:06: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 12:14:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 12:14:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.20_peaks.xls INFO @ Mon, 10 Aug 2020 12:14:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:14:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047576/SRX8047576.20_summits.bed INFO @ Mon, 10 Aug 2020 12:14:29: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (183 records, 4 fields): 4 millis CompletedMACS2peakCalling