Job ID = 8184556 SRX = SRX8047609 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:30:57 prefetch.2.10.7: 1) Downloading 'SRR11471333'... 2020-08-10T04:30:57 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:35:01 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:35:01 prefetch.2.10.7: 1) 'SRR11471333' was downloaded successfully Read 54298240 spots for SRR11471333/SRR11471333.sra Written 54298240 spots for SRR11471333/SRR11471333.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: 00:44:52 54298240 reads; of these: 54298240 (100.00%) were unpaired; of these: 1773553 (3.27%) aligned 0 times 39406761 (72.57%) aligned exactly 1 time 13117926 (24.16%) aligned >1 times 96.73% overall alignment rate Time searching: 00:44:54 Overall time: 00:44:54 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 24 files... [bam_rmdupse_core] 14288331 / 52524687 = 0.2720 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 14:34:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.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 14:34:59: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:34:59: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:35:04: 1000000 INFO @ Mon, 10 Aug 2020 14:35:10: 2000000 INFO @ Mon, 10 Aug 2020 14:35:15: 3000000 INFO @ Mon, 10 Aug 2020 14:35:20: 4000000 INFO @ Mon, 10 Aug 2020 14:35:25: 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 14:35:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.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 14:35:29: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:35:29: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:35:30: 6000000 INFO @ Mon, 10 Aug 2020 14:35:35: 1000000 INFO @ Mon, 10 Aug 2020 14:35:36: 7000000 INFO @ Mon, 10 Aug 2020 14:35:40: 2000000 INFO @ Mon, 10 Aug 2020 14:35:41: 8000000 INFO @ Mon, 10 Aug 2020 14:35:45: 3000000 INFO @ Mon, 10 Aug 2020 14:35:47: 9000000 INFO @ Mon, 10 Aug 2020 14:35:51: 4000000 INFO @ Mon, 10 Aug 2020 14:35:52: 10000000 INFO @ Mon, 10 Aug 2020 14:35:56: 5000000 INFO @ Mon, 10 Aug 2020 14:35:57: 11000000 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 14:35:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.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 14:35:59: #1 read tag files... INFO @ Mon, 10 Aug 2020 14:35:59: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 14:36:01: 6000000 INFO @ Mon, 10 Aug 2020 14:36:03: 12000000 INFO @ Mon, 10 Aug 2020 14:36:05: 1000000 INFO @ Mon, 10 Aug 2020 14:36:07: 7000000 INFO @ Mon, 10 Aug 2020 14:36:08: 13000000 INFO @ Mon, 10 Aug 2020 14:36:10: 2000000 INFO @ Mon, 10 Aug 2020 14:36:12: 8000000 INFO @ Mon, 10 Aug 2020 14:36:13: 14000000 INFO @ Mon, 10 Aug 2020 14:36:16: 3000000 INFO @ Mon, 10 Aug 2020 14:36:18: 9000000 INFO @ Mon, 10 Aug 2020 14:36:19: 15000000 INFO @ Mon, 10 Aug 2020 14:36:21: 4000000 INFO @ Mon, 10 Aug 2020 14:36:23: 10000000 INFO @ Mon, 10 Aug 2020 14:36:24: 16000000 INFO @ Mon, 10 Aug 2020 14:36:26: 5000000 INFO @ Mon, 10 Aug 2020 14:36:28: 11000000 INFO @ Mon, 10 Aug 2020 14:36:30: 17000000 INFO @ Mon, 10 Aug 2020 14:36:32: 6000000 INFO @ Mon, 10 Aug 2020 14:36:34: 12000000 INFO @ Mon, 10 Aug 2020 14:36:35: 18000000 INFO @ Mon, 10 Aug 2020 14:36:37: 7000000 INFO @ Mon, 10 Aug 2020 14:36:39: 13000000 INFO @ Mon, 10 Aug 2020 14:36:40: 19000000 INFO @ Mon, 10 Aug 2020 14:36:43: 8000000 INFO @ Mon, 10 Aug 2020 14:36:45: 14000000 INFO @ Mon, 10 Aug 2020 14:36:46: 20000000 INFO @ Mon, 10 Aug 2020 14:36:48: 9000000 INFO @ Mon, 10 Aug 2020 14:36:50: 15000000 INFO @ Mon, 10 Aug 2020 14:36:51: 21000000 INFO @ Mon, 10 Aug 2020 14:36:53: 10000000 INFO @ Mon, 10 Aug 2020 14:36:55: 16000000 INFO @ Mon, 10 Aug 2020 14:36:57: 22000000 INFO @ Mon, 10 Aug 2020 14:36:59: 11000000 INFO @ Mon, 10 Aug 2020 14:37:01: 17000000 INFO @ Mon, 10 Aug 2020 14:37:02: 23000000 INFO @ Mon, 10 Aug 2020 14:37:04: 12000000 INFO @ Mon, 10 Aug 2020 14:37:06: 18000000 INFO @ Mon, 10 Aug 2020 14:37:08: 24000000 INFO @ Mon, 10 Aug 2020 14:37:10: 13000000 INFO @ Mon, 10 Aug 2020 14:37:12: 19000000 INFO @ Mon, 10 Aug 2020 14:37:13: 25000000 INFO @ Mon, 10 Aug 2020 14:37:15: 14000000 INFO @ Mon, 10 Aug 2020 14:37:17: 20000000 INFO @ Mon, 10 Aug 2020 14:37:19: 26000000 INFO @ Mon, 10 Aug 2020 14:37:21: 15000000 INFO @ Mon, 10 Aug 2020 14:37:23: 21000000 INFO @ Mon, 10 Aug 2020 14:37:24: 27000000 INFO @ Mon, 10 Aug 2020 14:37:26: 16000000 INFO @ Mon, 10 Aug 2020 14:37:28: 22000000 INFO @ Mon, 10 Aug 2020 14:37:30: 28000000 INFO @ Mon, 10 Aug 2020 14:37:32: 17000000 INFO @ Mon, 10 Aug 2020 14:37:34: 23000000 INFO @ Mon, 10 Aug 2020 14:37:36: 29000000 INFO @ Mon, 10 Aug 2020 14:37:38: 18000000 INFO @ Mon, 10 Aug 2020 14:37:40: 24000000 INFO @ Mon, 10 Aug 2020 14:37:41: 30000000 INFO @ Mon, 10 Aug 2020 14:37:43: 19000000 INFO @ Mon, 10 Aug 2020 14:37:45: 25000000 INFO @ Mon, 10 Aug 2020 14:37:47: 31000000 INFO @ Mon, 10 Aug 2020 14:37:49: 20000000 INFO @ Mon, 10 Aug 2020 14:37:51: 26000000 INFO @ Mon, 10 Aug 2020 14:37:52: 32000000 INFO @ Mon, 10 Aug 2020 14:37:54: 21000000 INFO @ Mon, 10 Aug 2020 14:37:56: 27000000 INFO @ Mon, 10 Aug 2020 14:37:58: 33000000 INFO @ Mon, 10 Aug 2020 14:38:00: 22000000 INFO @ Mon, 10 Aug 2020 14:38:02: 28000000 INFO @ Mon, 10 Aug 2020 14:38:03: 34000000 INFO @ Mon, 10 Aug 2020 14:38:06: 23000000 INFO @ Mon, 10 Aug 2020 14:38:08: 29000000 INFO @ Mon, 10 Aug 2020 14:38:09: 35000000 INFO @ Mon, 10 Aug 2020 14:38:12: 24000000 INFO @ Mon, 10 Aug 2020 14:38:13: 30000000 INFO @ Mon, 10 Aug 2020 14:38:14: 36000000 INFO @ Mon, 10 Aug 2020 14:38:17: 25000000 INFO @ Mon, 10 Aug 2020 14:38:19: 31000000 INFO @ Mon, 10 Aug 2020 14:38:20: 37000000 INFO @ Mon, 10 Aug 2020 14:38:23: 26000000 INFO @ Mon, 10 Aug 2020 14:38:24: 32000000 INFO @ Mon, 10 Aug 2020 14:38:26: 38000000 INFO @ Mon, 10 Aug 2020 14:38:27: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:38:27: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:38:27: #1 total tags in treatment: 38236356 INFO @ Mon, 10 Aug 2020 14:38:27: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:38:27: #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 14:38:28: #1 tags after filtering in treatment: 38236273 INFO @ Mon, 10 Aug 2020 14:38:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:38:28: #1 finished! INFO @ Mon, 10 Aug 2020 14:38:28: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:38:29: 27000000 INFO @ Mon, 10 Aug 2020 14:38:30: 33000000 INFO @ Mon, 10 Aug 2020 14:38:31: #2 number of paired peaks: 11245 INFO @ Mon, 10 Aug 2020 14:38:31: start model_add_line... INFO @ Mon, 10 Aug 2020 14:38:32: start X-correlation... INFO @ Mon, 10 Aug 2020 14:38:32: end of X-cor INFO @ Mon, 10 Aug 2020 14:38:32: #2 finished! INFO @ Mon, 10 Aug 2020 14:38:32: #2 predicted fragment length is 85 bps INFO @ Mon, 10 Aug 2020 14:38:32: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 10 Aug 2020 14:38:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.05_model.r WARNING @ Mon, 10 Aug 2020 14:38:32: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:38:32: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Mon, 10 Aug 2020 14:38:32: #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 14:38:32: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:38:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:38:34: 28000000 INFO @ Mon, 10 Aug 2020 14:38:35: 34000000 INFO @ Mon, 10 Aug 2020 14:38:40: 29000000 INFO @ Mon, 10 Aug 2020 14:38:41: 35000000 INFO @ Mon, 10 Aug 2020 14:38:45: 30000000 INFO @ Mon, 10 Aug 2020 14:38:46: 36000000 INFO @ Mon, 10 Aug 2020 14:38:50: 31000000 INFO @ Mon, 10 Aug 2020 14:38:52: 37000000 INFO @ Mon, 10 Aug 2020 14:38:56: 32000000 INFO @ Mon, 10 Aug 2020 14:38:58: 38000000 INFO @ Mon, 10 Aug 2020 14:38:59: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:38:59: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:38:59: #1 total tags in treatment: 38236356 INFO @ Mon, 10 Aug 2020 14:38:59: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:38:59: #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 14:39:00: #1 tags after filtering in treatment: 38236273 INFO @ Mon, 10 Aug 2020 14:39:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:39:00: #1 finished! INFO @ Mon, 10 Aug 2020 14:39:00: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:39:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:39:01: 33000000 INFO @ Mon, 10 Aug 2020 14:39:03: #2 number of paired peaks: 11245 INFO @ Mon, 10 Aug 2020 14:39:03: start model_add_line... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 14:39:04: start X-correlation... INFO @ Mon, 10 Aug 2020 14:39:04: end of X-cor INFO @ Mon, 10 Aug 2020 14:39:04: #2 finished! INFO @ Mon, 10 Aug 2020 14:39:04: #2 predicted fragment length is 85 bps INFO @ Mon, 10 Aug 2020 14:39:04: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 10 Aug 2020 14:39:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.10_model.r WARNING @ Mon, 10 Aug 2020 14:39:04: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:39:04: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Mon, 10 Aug 2020 14:39:04: #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 14:39:04: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:39:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:39:07: 34000000 INFO @ Mon, 10 Aug 2020 14:39:12: 35000000 INFO @ Mon, 10 Aug 2020 14:39:17: 36000000 INFO @ Mon, 10 Aug 2020 14:39:23: 37000000 INFO @ Mon, 10 Aug 2020 14:39:28: 38000000 INFO @ Mon, 10 Aug 2020 14:39:29: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 14:39:29: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 14:39:29: #1 total tags in treatment: 38236356 INFO @ Mon, 10 Aug 2020 14:39:29: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 14:39:29: #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 14:39:30: #1 tags after filtering in treatment: 38236273 INFO @ Mon, 10 Aug 2020 14:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 14:39:30: #1 finished! INFO @ Mon, 10 Aug 2020 14:39:30: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 14:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 14:39:33: #2 number of paired peaks: 11245 INFO @ Mon, 10 Aug 2020 14:39:33: start model_add_line... INFO @ Mon, 10 Aug 2020 14:39:33: start X-correlation... INFO @ Mon, 10 Aug 2020 14:39:34: end of X-cor INFO @ Mon, 10 Aug 2020 14:39:34: #2 finished! INFO @ Mon, 10 Aug 2020 14:39:34: #2 predicted fragment length is 85 bps INFO @ Mon, 10 Aug 2020 14:39:34: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 10 Aug 2020 14:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.20_model.r WARNING @ Mon, 10 Aug 2020 14:39:34: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 14:39:34: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Mon, 10 Aug 2020 14:39:34: #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 14:39:34: #3 Call peaks... INFO @ Mon, 10 Aug 2020 14:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 14:39:56: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:40:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 14:40:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.05_peaks.xls INFO @ Mon, 10 Aug 2020 14:40:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:40:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.05_summits.bed INFO @ Mon, 10 Aug 2020 14:40:40: Done! pass1 - making usageList (98 chroms): 1 millis pass2 - checking and writing primary data (4725 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:40:57: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 14:41:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.10_peaks.xls INFO @ Mon, 10 Aug 2020 14:41:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:41:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.10_summits.bed INFO @ Mon, 10 Aug 2020 14:41:10: Done! pass1 - making usageList (64 chroms): 1 millis pass2 - checking and writing primary data (1723 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 14:41:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.20_peaks.xls INFO @ Mon, 10 Aug 2020 14:41:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 14:41:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047609/SRX8047609.20_summits.bed INFO @ Mon, 10 Aug 2020 14:41:41: Done! pass1 - making usageList (49 chroms): 0 millis pass2 - checking and writing primary data (587 records, 4 fields): 4 millis CompletedMACS2peakCalling