Job ID = 8184616 SRX = SRX8047626 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:56:53 prefetch.2.10.7: 1) Downloading 'SRR11471350'... 2020-08-10T04:56:53 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:58:55 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:58:55 prefetch.2.10.7: 1) 'SRR11471350' was downloaded successfully Read 38703415 spots for SRR11471350/SRR11471350.sra Written 38703415 spots for SRR11471350/SRR11471350.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: 00:34:47 38703415 reads; of these: 38703415 (100.00%) were unpaired; of these: 956377 (2.47%) aligned 0 times 26729706 (69.06%) aligned exactly 1 time 11017332 (28.47%) aligned >1 times 97.53% overall alignment rate Time searching: 00:34:51 Overall time: 00:34:51 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 16 files... [bam_rmdupse_core] 2118101 / 37747038 = 0.0561 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 14:47:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.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 14:47:00: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:47:00: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:47:05: 1000000 INFO @ Mon, 10 Aug 2020 14:47:10: 2000000 INFO @ Mon, 10 Aug 2020 14:47:16: 3000000 INFO @ Mon, 10 Aug 2020 14:47:21: 4000000 INFO @ Mon, 10 Aug 2020 14:47:26: 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 14:47:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.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 14:47:30: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:47:30: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:47:32: 6000000 INFO @ Mon, 10 Aug 2020 14:47:35: 1000000 INFO @ Mon, 10 Aug 2020 14:47:37: 7000000 INFO @ Mon, 10 Aug 2020 14:47:40: 2000000 INFO @ Mon, 10 Aug 2020 14:47:43: 8000000 INFO @ Mon, 10 Aug 2020 14:47:46: 3000000 INFO @ Mon, 10 Aug 2020 14:47:48: 9000000 INFO @ Mon, 10 Aug 2020 14:47:51: 4000000 INFO @ Mon, 10 Aug 2020 14:47:53: 10000000 INFO @ Mon, 10 Aug 2020 14:47:56: 5000000 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 14:47:59: 11000000 INFO @ Mon, 10 Aug 2020 14:48:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.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 14:48:00: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:48:00: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:48:02: 6000000 INFO @ Mon, 10 Aug 2020 14:48:04: 12000000 INFO @ Mon, 10 Aug 2020 14:48:05: 1000000 INFO @ Mon, 10 Aug 2020 14:48:07: 7000000 INFO @ Mon, 10 Aug 2020 14:48:09: 13000000 INFO @ Mon, 10 Aug 2020 14:48:11: 2000000 INFO @ Mon, 10 Aug 2020 14:48:13: 8000000 INFO @ Mon, 10 Aug 2020 14:48:15: 14000000 INFO @ Mon, 10 Aug 2020 14:48:16: 3000000 INFO @ Mon, 10 Aug 2020 14:48:19: 9000000 INFO @ Mon, 10 Aug 2020 14:48:21: 15000000 INFO @ Mon, 10 Aug 2020 14:48:22: 4000000 INFO @ Mon, 10 Aug 2020 14:48:24: 10000000 INFO @ Mon, 10 Aug 2020 14:48:26: 16000000 INFO @ Mon, 10 Aug 2020 14:48:28: 5000000 INFO @ Mon, 10 Aug 2020 14:48:30: 11000000 INFO @ Mon, 10 Aug 2020 14:48:32: 17000000 INFO @ Mon, 10 Aug 2020 14:48:33: 6000000 INFO @ Mon, 10 Aug 2020 14:48:35: 12000000 INFO @ Mon, 10 Aug 2020 14:48:37: 18000000 INFO @ Mon, 10 Aug 2020 14:48:39: 7000000 INFO @ Mon, 10 Aug 2020 14:48:41: 13000000 INFO @ Mon, 10 Aug 2020 14:48:43: 19000000 INFO @ Mon, 10 Aug 2020 14:48:44: 8000000 INFO @ Mon, 10 Aug 2020 14:48:46: 14000000 INFO @ Mon, 10 Aug 2020 14:48:49: 20000000 INFO @ Mon, 10 Aug 2020 14:48:50: 9000000 INFO @ Mon, 10 Aug 2020 14:48:52: 15000000 INFO @ Mon, 10 Aug 2020 14:48:54: 21000000 INFO @ Mon, 10 Aug 2020 14:48:55: 10000000 INFO @ Mon, 10 Aug 2020 14:48:57: 16000000 INFO @ Mon, 10 Aug 2020 14:49:00: 22000000 INFO @ Mon, 10 Aug 2020 14:49:01: 11000000 INFO @ Mon, 10 Aug 2020 14:49:03: 17000000 INFO @ Mon, 10 Aug 2020 14:49:05: 23000000 INFO @ Mon, 10 Aug 2020 14:49:06: 12000000 INFO @ Mon, 10 Aug 2020 14:49:08: 18000000 INFO @ Mon, 10 Aug 2020 14:49:10: 24000000 INFO @ Mon, 10 Aug 2020 14:49:12: 13000000 INFO @ Mon, 10 Aug 2020 14:49:14: 19000000 INFO @ Mon, 10 Aug 2020 14:49:16: 25000000 INFO @ Mon, 10 Aug 2020 14:49:17: 14000000 INFO @ Mon, 10 Aug 2020 14:49:19: 20000000 INFO @ Mon, 10 Aug 2020 14:49:22: 26000000 INFO @ Mon, 10 Aug 2020 14:49:23: 15000000 INFO @ Mon, 10 Aug 2020 14:49:25: 21000000 INFO @ Mon, 10 Aug 2020 14:49:27: 27000000 INFO @ Mon, 10 Aug 2020 14:49:28: 16000000 INFO @ Mon, 10 Aug 2020 14:49:30: 22000000 INFO @ Mon, 10 Aug 2020 14:49:33: 28000000 INFO @ Mon, 10 Aug 2020 14:49:34: 17000000 INFO @ Mon, 10 Aug 2020 14:49:36: 23000000 INFO @ Mon, 10 Aug 2020 14:49:38: 29000000 INFO @ Mon, 10 Aug 2020 14:49:39: 18000000 INFO @ Mon, 10 Aug 2020 14:49:41: 24000000 INFO @ Mon, 10 Aug 2020 14:49:43: 30000000 INFO @ Mon, 10 Aug 2020 14:49:45: 19000000 INFO @ Mon, 10 Aug 2020 14:49:47: 25000000 INFO @ Mon, 10 Aug 2020 14:49:49: 31000000 INFO @ Mon, 10 Aug 2020 14:49:50: 20000000 INFO @ Mon, 10 Aug 2020 14:49:52: 26000000 INFO @ Mon, 10 Aug 2020 14:49:54: 32000000 INFO @ Mon, 10 Aug 2020 14:49:56: 21000000 INFO @ Mon, 10 Aug 2020 14:49:58: 27000000 INFO @ Mon, 10 Aug 2020 14:50:00: 33000000 INFO @ Mon, 10 Aug 2020 14:50:01: 22000000 INFO @ Mon, 10 Aug 2020 14:50:03: 28000000 INFO @ Mon, 10 Aug 2020 14:50:06: 34000000 INFO @ Mon, 10 Aug 2020 14:50:07: 23000000 INFO @ Mon, 10 Aug 2020 14:50:08: 29000000 INFO @ Mon, 10 Aug 2020 14:50:11: 35000000 INFO @ Mon, 10 Aug 2020 14:50:12: 24000000 INFO @ Mon, 10 Aug 2020 14:50:14: 30000000 INFO @ Mon, 10 Aug 2020 14:50:15: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:50:15: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:50:15: #1 total tags in treatment: 35628937 INFO @ Mon, 10 Aug 2020 14:50:15: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:50:15: #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 14:50:16: #1 tags after filtering in treatment: 35628856 INFO @ Mon, 10 Aug 2020 14:50:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:50:16: #1 finished! INFO @ Mon, 10 Aug 2020 14:50:16: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:50:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:50:18: 25000000 INFO @ Mon, 10 Aug 2020 14:50:19: #2 number of paired peaks: 6040 INFO @ Mon, 10 Aug 2020 14:50:19: start model_add_line... INFO @ Mon, 10 Aug 2020 14:50:19: 31000000 INFO @ Mon, 10 Aug 2020 14:50:19: start X-correlation... INFO @ Mon, 10 Aug 2020 14:50:20: end of X-cor INFO @ Mon, 10 Aug 2020 14:50:20: #2 finished! INFO @ Mon, 10 Aug 2020 14:50:20: #2 predicted fragment length is 52 bps INFO @ Mon, 10 Aug 2020 14:50:20: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 10 Aug 2020 14:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.05_model.r WARNING @ Mon, 10 Aug 2020 14:50:20: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:50:20: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 10 Aug 2020 14:50:20: #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 14:50:20: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:50:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:50:23: 26000000 INFO @ Mon, 10 Aug 2020 14:50:25: 32000000 INFO @ Mon, 10 Aug 2020 14:50:29: 27000000 INFO @ Mon, 10 Aug 2020 14:50:31: 33000000 INFO @ Mon, 10 Aug 2020 14:50:34: 28000000 INFO @ Mon, 10 Aug 2020 14:50:36: 34000000 INFO @ Mon, 10 Aug 2020 14:50:40: 29000000 INFO @ Mon, 10 Aug 2020 14:50:42: 35000000 INFO @ Mon, 10 Aug 2020 14:50:45: 30000000 INFO @ Mon, 10 Aug 2020 14:50:45: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:50:45: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:50:45: #1 total tags in treatment: 35628937 INFO @ Mon, 10 Aug 2020 14:50:45: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:50:45: #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 14:50:46: #1 tags after filtering in treatment: 35628856 INFO @ Mon, 10 Aug 2020 14:50:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:50:46: #1 finished! INFO @ Mon, 10 Aug 2020 14:50:46: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:50:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:50:49: #2 number of paired peaks: 6040 INFO @ Mon, 10 Aug 2020 14:50:49: start model_add_line... INFO @ Mon, 10 Aug 2020 14:50:50: start X-correlation... INFO @ Mon, 10 Aug 2020 14:50:50: end of X-cor INFO @ Mon, 10 Aug 2020 14:50:50: #2 finished! INFO @ Mon, 10 Aug 2020 14:50:50: #2 predicted fragment length is 52 bps INFO @ Mon, 10 Aug 2020 14:50:50: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 10 Aug 2020 14:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.10_model.r WARNING @ Mon, 10 Aug 2020 14:50:50: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:50:50: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 10 Aug 2020 14:50:50: #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 14:50:50: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:50:51: 31000000 INFO @ Mon, 10 Aug 2020 14:50:56: 32000000 INFO @ Mon, 10 Aug 2020 14:51:02: 33000000 INFO @ Mon, 10 Aug 2020 14:51:07: 34000000 INFO @ Mon, 10 Aug 2020 14:51:13: 35000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:51:16: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:51:16: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:51:16: #1 total tags in treatment: 35628937 INFO @ Mon, 10 Aug 2020 14:51:16: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:51:16: #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 14:51:17: #1 tags after filtering in treatment: 35628856 INFO @ Mon, 10 Aug 2020 14:51:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:51:17: #1 finished! INFO @ Mon, 10 Aug 2020 14:51:17: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:51:20: #2 number of paired peaks: 6040 INFO @ Mon, 10 Aug 2020 14:51:20: start model_add_line... INFO @ Mon, 10 Aug 2020 14:51:20: start X-correlation... INFO @ Mon, 10 Aug 2020 14:51:20: end of X-cor INFO @ Mon, 10 Aug 2020 14:51:20: #2 finished! INFO @ Mon, 10 Aug 2020 14:51:20: #2 predicted fragment length is 52 bps INFO @ Mon, 10 Aug 2020 14:51:20: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 10 Aug 2020 14:51:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.20_model.r WARNING @ Mon, 10 Aug 2020 14:51:20: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:51:20: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 10 Aug 2020 14:51:20: #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 14:51:20: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:51:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:51:39: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:52:09: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:52:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:52:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:52:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.05_summits.bed INFO @ Mon, 10 Aug 2020 14:52:20: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (3414 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:52:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:52:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:52:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:52:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.10_summits.bed INFO @ Mon, 10 Aug 2020 14:52:50: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (1550 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:53:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:53:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047626/SRX8047626.20_summits.bed INFO @ Mon, 10 Aug 2020 14:53:20: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (680 records, 4 fields): 3 millis CompletedMACS2peakCalling