Job ID = 8184614 SRX = SRX8047625 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:56:37 prefetch.2.10.7: 1) Downloading 'SRR11471349'... 2020-08-10T04:56:37 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:59:26 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:59:26 prefetch.2.10.7: 1) 'SRR11471349' was downloaded successfully Read 39839675 spots for SRR11471349/SRR11471349.sra Written 39839675 spots for SRR11471349/SRR11471349.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: 00:00:01 Multiseed full-index search: 00:31:35 39839675 reads; of these: 39839675 (100.00%) were unpaired; of these: 1000102 (2.51%) aligned 0 times 27617861 (69.32%) aligned exactly 1 time 11221712 (28.17%) aligned >1 times 97.49% overall alignment rate Time searching: 00:31:37 Overall time: 00:31:37 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] 3793639 / 38839573 = 0.0977 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 14:43:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.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 14:43:21: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:43:21: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:43:27: 1000000 INFO @ Mon, 10 Aug 2020 14:43:34: 2000000 INFO @ Mon, 10 Aug 2020 14:43:41: 3000000 INFO @ Mon, 10 Aug 2020 14:43:47: 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 14:43:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.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 14:43:50: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:43:50: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:43:54: 5000000 INFO @ Mon, 10 Aug 2020 14:43:58: 1000000 INFO @ Mon, 10 Aug 2020 14:44:01: 6000000 INFO @ Mon, 10 Aug 2020 14:44:04: 2000000 INFO @ Mon, 10 Aug 2020 14:44:08: 7000000 INFO @ Mon, 10 Aug 2020 14:44:11: 3000000 INFO @ Mon, 10 Aug 2020 14:44:15: 8000000 INFO @ Mon, 10 Aug 2020 14:44:18: 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 14:44:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.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 14:44:21: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:44:21: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:44:22: 9000000 INFO @ Mon, 10 Aug 2020 14:44:25: 5000000 INFO @ Mon, 10 Aug 2020 14:44:27: 1000000 INFO @ Mon, 10 Aug 2020 14:44:29: 10000000 INFO @ Mon, 10 Aug 2020 14:44:32: 6000000 INFO @ Mon, 10 Aug 2020 14:44:33: 2000000 INFO @ Mon, 10 Aug 2020 14:44:36: 11000000 INFO @ Mon, 10 Aug 2020 14:44:39: 7000000 INFO @ Mon, 10 Aug 2020 14:44:40: 3000000 INFO @ Mon, 10 Aug 2020 14:44:43: 12000000 INFO @ Mon, 10 Aug 2020 14:44:46: 4000000 INFO @ Mon, 10 Aug 2020 14:44:47: 8000000 INFO @ Mon, 10 Aug 2020 14:44:50: 13000000 INFO @ Mon, 10 Aug 2020 14:44:52: 5000000 INFO @ Mon, 10 Aug 2020 14:44:54: 9000000 INFO @ Mon, 10 Aug 2020 14:44:58: 14000000 INFO @ Mon, 10 Aug 2020 14:44:59: 6000000 INFO @ Mon, 10 Aug 2020 14:45:01: 10000000 INFO @ Mon, 10 Aug 2020 14:45:04: 15000000 INFO @ Mon, 10 Aug 2020 14:45:05: 7000000 INFO @ Mon, 10 Aug 2020 14:45:08: 11000000 INFO @ Mon, 10 Aug 2020 14:45:11: 8000000 INFO @ Mon, 10 Aug 2020 14:45:11: 16000000 INFO @ Mon, 10 Aug 2020 14:45:15: 12000000 INFO @ Mon, 10 Aug 2020 14:45:18: 9000000 INFO @ Mon, 10 Aug 2020 14:45:18: 17000000 INFO @ Mon, 10 Aug 2020 14:45:22: 13000000 INFO @ Mon, 10 Aug 2020 14:45:24: 10000000 INFO @ Mon, 10 Aug 2020 14:45:25: 18000000 INFO @ Mon, 10 Aug 2020 14:45:29: 14000000 INFO @ Mon, 10 Aug 2020 14:45:30: 11000000 INFO @ Mon, 10 Aug 2020 14:45:32: 19000000 INFO @ Mon, 10 Aug 2020 14:45:36: 15000000 INFO @ Mon, 10 Aug 2020 14:45:37: 12000000 INFO @ Mon, 10 Aug 2020 14:45:39: 20000000 INFO @ Mon, 10 Aug 2020 14:45:43: 16000000 INFO @ Mon, 10 Aug 2020 14:45:43: 13000000 INFO @ Mon, 10 Aug 2020 14:45:46: 21000000 INFO @ Mon, 10 Aug 2020 14:45:49: 14000000 INFO @ Mon, 10 Aug 2020 14:45:50: 17000000 INFO @ Mon, 10 Aug 2020 14:45:53: 22000000 INFO @ Mon, 10 Aug 2020 14:45:56: 15000000 INFO @ Mon, 10 Aug 2020 14:45:57: 18000000 INFO @ Mon, 10 Aug 2020 14:46:00: 23000000 INFO @ Mon, 10 Aug 2020 14:46:02: 16000000 INFO @ Mon, 10 Aug 2020 14:46:04: 19000000 INFO @ Mon, 10 Aug 2020 14:46:07: 24000000 INFO @ Mon, 10 Aug 2020 14:46:08: 17000000 INFO @ Mon, 10 Aug 2020 14:46:11: 20000000 INFO @ Mon, 10 Aug 2020 14:46:14: 25000000 INFO @ Mon, 10 Aug 2020 14:46:15: 18000000 INFO @ Mon, 10 Aug 2020 14:46:18: 21000000 INFO @ Mon, 10 Aug 2020 14:46:21: 19000000 INFO @ Mon, 10 Aug 2020 14:46:21: 26000000 INFO @ Mon, 10 Aug 2020 14:46:25: 22000000 INFO @ Mon, 10 Aug 2020 14:46:27: 20000000 INFO @ Mon, 10 Aug 2020 14:46:28: 27000000 INFO @ Mon, 10 Aug 2020 14:46:32: 23000000 INFO @ Mon, 10 Aug 2020 14:46:34: 21000000 INFO @ Mon, 10 Aug 2020 14:46:35: 28000000 INFO @ Mon, 10 Aug 2020 14:46:39: 24000000 INFO @ Mon, 10 Aug 2020 14:46:40: 22000000 INFO @ Mon, 10 Aug 2020 14:46:42: 29000000 INFO @ Mon, 10 Aug 2020 14:46:46: 25000000 INFO @ Mon, 10 Aug 2020 14:46:46: 23000000 INFO @ Mon, 10 Aug 2020 14:46:49: 30000000 INFO @ Mon, 10 Aug 2020 14:46:52: 24000000 INFO @ Mon, 10 Aug 2020 14:46:53: 26000000 INFO @ Mon, 10 Aug 2020 14:46:56: 31000000 INFO @ Mon, 10 Aug 2020 14:46:59: 25000000 INFO @ Mon, 10 Aug 2020 14:47:00: 27000000 INFO @ Mon, 10 Aug 2020 14:47:03: 32000000 INFO @ Mon, 10 Aug 2020 14:47:05: 26000000 INFO @ Mon, 10 Aug 2020 14:47:07: 28000000 INFO @ Mon, 10 Aug 2020 14:47:10: 33000000 INFO @ Mon, 10 Aug 2020 14:47:11: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:47:13: 29000000 INFO @ Mon, 10 Aug 2020 14:47:17: 34000000 INFO @ Mon, 10 Aug 2020 14:47:18: 28000000 INFO @ Mon, 10 Aug 2020 14:47:21: 30000000 INFO @ Mon, 10 Aug 2020 14:47:24: 29000000 INFO @ Mon, 10 Aug 2020 14:47:24: 35000000 INFO @ Mon, 10 Aug 2020 14:47:25: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:47:25: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:47:25: #1 total tags in treatment: 35045934 INFO @ Mon, 10 Aug 2020 14:47:25: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:47:25: #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 14:47:26: #1 tags after filtering in treatment: 35045847 INFO @ Mon, 10 Aug 2020 14:47:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:47:26: #1 finished! INFO @ Mon, 10 Aug 2020 14:47:26: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:47:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:47:28: 31000000 INFO @ Mon, 10 Aug 2020 14:47:29: #2 number of paired peaks: 6115 INFO @ Mon, 10 Aug 2020 14:47:29: start model_add_line... INFO @ Mon, 10 Aug 2020 14:47:29: start X-correlation... INFO @ Mon, 10 Aug 2020 14:47:29: end of X-cor INFO @ Mon, 10 Aug 2020 14:47:29: #2 finished! INFO @ Mon, 10 Aug 2020 14:47:29: #2 predicted fragment length is 52 bps INFO @ Mon, 10 Aug 2020 14:47:29: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 10 Aug 2020 14:47:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.05_model.r WARNING @ Mon, 10 Aug 2020 14:47:29: #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 14:47:29: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 10 Aug 2020 14:47:29: #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 14:47:29: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:47:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:47:31: 30000000 INFO @ Mon, 10 Aug 2020 14:47:35: 32000000 INFO @ Mon, 10 Aug 2020 14:47:37: 31000000 INFO @ Mon, 10 Aug 2020 14:47:42: 33000000 INFO @ Mon, 10 Aug 2020 14:47:43: 32000000 INFO @ Mon, 10 Aug 2020 14:47:49: 34000000 INFO @ Mon, 10 Aug 2020 14:47:50: 33000000 INFO @ Mon, 10 Aug 2020 14:47:56: 35000000 INFO @ Mon, 10 Aug 2020 14:47:56: 34000000 INFO @ Mon, 10 Aug 2020 14:47:56: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:47:56: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:47:56: #1 total tags in treatment: 35045934 INFO @ Mon, 10 Aug 2020 14:47:56: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:47:56: #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 14:47:57: #1 tags after filtering in treatment: 35045847 INFO @ Mon, 10 Aug 2020 14:47:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:47:57: #1 finished! INFO @ Mon, 10 Aug 2020 14:47:57: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:47:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:48:00: #2 number of paired peaks: 6115 INFO @ Mon, 10 Aug 2020 14:48:00: start model_add_line... INFO @ Mon, 10 Aug 2020 14:48:00: start X-correlation... INFO @ Mon, 10 Aug 2020 14:48:00: end of X-cor INFO @ Mon, 10 Aug 2020 14:48:00: #2 finished! INFO @ Mon, 10 Aug 2020 14:48:00: #2 predicted fragment length is 52 bps INFO @ Mon, 10 Aug 2020 14:48:00: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 10 Aug 2020 14:48:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.10_model.r WARNING @ Mon, 10 Aug 2020 14:48:00: #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 14:48:00: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 10 Aug 2020 14:48:00: #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 14:48:00: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:48:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:48:02: 35000000 INFO @ Mon, 10 Aug 2020 14:48:02: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:48:02: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:48:02: #1 total tags in treatment: 35045934 INFO @ Mon, 10 Aug 2020 14:48:02: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:48:02: #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 14:48:03: #1 tags after filtering in treatment: 35045847 INFO @ Mon, 10 Aug 2020 14:48:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:48:03: #1 finished! INFO @ Mon, 10 Aug 2020 14:48:03: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:48:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:48:06: #2 number of paired peaks: 6115 INFO @ Mon, 10 Aug 2020 14:48:06: start model_add_line... INFO @ Mon, 10 Aug 2020 14:48:06: start X-correlation... INFO @ Mon, 10 Aug 2020 14:48:06: end of X-cor INFO @ Mon, 10 Aug 2020 14:48:06: #2 finished! INFO @ Mon, 10 Aug 2020 14:48:06: #2 predicted fragment length is 52 bps INFO @ Mon, 10 Aug 2020 14:48:06: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 10 Aug 2020 14:48:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.20_model.r WARNING @ Mon, 10 Aug 2020 14:48:06: #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 14:48:06: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 10 Aug 2020 14:48:06: #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 14:48:06: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:48:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:48:46: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:49:18: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:49:24: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:49:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:49:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:49:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.05_summits.bed INFO @ Mon, 10 Aug 2020 14:49:24: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (2695 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:49:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:49:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:49:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.10_summits.bed INFO @ Mon, 10 Aug 2020 14:49:56: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (1389 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047625/SRX8047625.20_summits.bed INFO @ Mon, 10 Aug 2020 14:50:01: Done! pass1 - making usageList (35 chroms): 0 millis pass2 - checking and writing primary data (647 records, 4 fields): 3 millis CompletedMACS2peakCalling