Job ID = 8184547 SRX = SRX8047605 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:25:50 prefetch.2.10.7: 1) Downloading 'SRR11471329'... 2020-08-10T04:25:50 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:26:52 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:26:52 prefetch.2.10.7: 1) 'SRR11471329' was downloaded successfully Read 15284072 spots for SRR11471329/SRR11471329.sra Written 15284072 spots for SRR11471329/SRR11471329.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:58 15284072 reads; of these: 15284072 (100.00%) were unpaired; of these: 2026226 (13.26%) aligned 0 times 9986368 (65.34%) aligned exactly 1 time 3271478 (21.40%) aligned >1 times 86.74% overall alignment rate Time searching: 00:12:59 Overall time: 00:12:59 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] 4895520 / 13257846 = 0.3693 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 13:44:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.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 13:44:03: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:44:03: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:44:09: 1000000 INFO @ Mon, 10 Aug 2020 13:44:14: 2000000 INFO @ Mon, 10 Aug 2020 13:44:20: 3000000 INFO @ Mon, 10 Aug 2020 13:44:26: 4000000 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 13:44:32: 5000000 INFO @ Mon, 10 Aug 2020 13:44:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.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 13:44:32: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:44:32: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:44:38: 6000000 INFO @ Mon, 10 Aug 2020 13:44:39: 1000000 INFO @ Mon, 10 Aug 2020 13:44:45: 7000000 INFO @ Mon, 10 Aug 2020 13:44:45: 2000000 INFO @ Mon, 10 Aug 2020 13:44:51: 8000000 INFO @ Mon, 10 Aug 2020 13:44:52: 3000000 INFO @ Mon, 10 Aug 2020 13:44:54: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:44:54: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:44:54: #1 total tags in treatment: 8362326 INFO @ Mon, 10 Aug 2020 13:44:54: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:44:54: #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 13:44:54: #1 tags after filtering in treatment: 8362119 INFO @ Mon, 10 Aug 2020 13:44:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:44:54: #1 finished! INFO @ Mon, 10 Aug 2020 13:44:54: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:44:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:44:56: #2 number of paired peaks: 30932 INFO @ Mon, 10 Aug 2020 13:44:56: start model_add_line... INFO @ Mon, 10 Aug 2020 13:44:56: start X-correlation... INFO @ Mon, 10 Aug 2020 13:44:56: end of X-cor INFO @ Mon, 10 Aug 2020 13:44:56: #2 finished! INFO @ Mon, 10 Aug 2020 13:44:56: #2 predicted fragment length is 81 bps INFO @ Mon, 10 Aug 2020 13:44:56: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 10 Aug 2020 13:44:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.05_model.r WARNING @ Mon, 10 Aug 2020 13:44:56: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:44:56: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 10 Aug 2020 13:44:56: #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 13:44:56: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:44:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:44:58: 4000000 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 13:45:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.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 13:45:02: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:45:02: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:45:04: 5000000 INFO @ Mon, 10 Aug 2020 13:45:10: 1000000 INFO @ Mon, 10 Aug 2020 13:45:11: 6000000 INFO @ Mon, 10 Aug 2020 13:45:14: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:45:18: 2000000 INFO @ Mon, 10 Aug 2020 13:45:18: 7000000 INFO @ Mon, 10 Aug 2020 13:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.05_summits.bed INFO @ Mon, 10 Aug 2020 13:45:23: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (1350 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:45:25: 8000000 INFO @ Mon, 10 Aug 2020 13:45:25: 3000000 INFO @ Mon, 10 Aug 2020 13:45:28: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:45:28: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:45:28: #1 total tags in treatment: 8362326 INFO @ Mon, 10 Aug 2020 13:45:28: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:45:28: #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 13:45:28: #1 tags after filtering in treatment: 8362119 INFO @ Mon, 10 Aug 2020 13:45:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:45:28: #1 finished! INFO @ Mon, 10 Aug 2020 13:45:28: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:45:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:45:30: #2 number of paired peaks: 30932 INFO @ Mon, 10 Aug 2020 13:45:30: start model_add_line... INFO @ Mon, 10 Aug 2020 13:45:30: start X-correlation... INFO @ Mon, 10 Aug 2020 13:45:30: end of X-cor INFO @ Mon, 10 Aug 2020 13:45:30: #2 finished! INFO @ Mon, 10 Aug 2020 13:45:30: #2 predicted fragment length is 81 bps INFO @ Mon, 10 Aug 2020 13:45:30: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 10 Aug 2020 13:45:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.10_model.r WARNING @ Mon, 10 Aug 2020 13:45:30: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:45:30: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 10 Aug 2020 13:45:30: #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 13:45:30: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:45:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:45:33: 4000000 INFO @ Mon, 10 Aug 2020 13:45:40: 5000000 INFO @ Mon, 10 Aug 2020 13:45:47: 6000000 INFO @ Mon, 10 Aug 2020 13:45:49: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:45:54: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.10_summits.bed INFO @ Mon, 10 Aug 2020 13:45:58: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (528 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:46:01: 8000000 INFO @ Mon, 10 Aug 2020 13:46:03: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:46:03: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:46:03: #1 total tags in treatment: 8362326 INFO @ Mon, 10 Aug 2020 13:46:03: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:46:03: #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 13:46:03: #1 tags after filtering in treatment: 8362119 INFO @ Mon, 10 Aug 2020 13:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:46:03: #1 finished! INFO @ Mon, 10 Aug 2020 13:46:03: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:46:05: #2 number of paired peaks: 30932 INFO @ Mon, 10 Aug 2020 13:46:05: start model_add_line... INFO @ Mon, 10 Aug 2020 13:46:05: start X-correlation... INFO @ Mon, 10 Aug 2020 13:46:05: end of X-cor INFO @ Mon, 10 Aug 2020 13:46:05: #2 finished! INFO @ Mon, 10 Aug 2020 13:46:05: #2 predicted fragment length is 81 bps INFO @ Mon, 10 Aug 2020 13:46:05: #2 alternative fragment length(s) may be 81 bps INFO @ Mon, 10 Aug 2020 13:46:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.20_model.r WARNING @ Mon, 10 Aug 2020 13:46:05: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:46:05: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Mon, 10 Aug 2020 13:46:05: #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 13:46:05: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:46:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:46:24: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:46:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:46:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047605/SRX8047605.20_summits.bed INFO @ Mon, 10 Aug 2020 13:46:34: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (196 records, 4 fields): 2 millis CompletedMACS2peakCalling