Job ID = 6498672 SRX = SRX685464 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:27:16 prefetch.2.10.7: 1) Downloading 'SRR1556386'... 2020-06-26T00:27:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:30:56 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:30:56 prefetch.2.10.7: 1) 'SRR1556386' was downloaded successfully Read 44707678 spots for SRR1556386/SRR1556386.sra Written 44707678 spots for SRR1556386/SRR1556386.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:14 44707678 reads; of these: 44707678 (100.00%) were unpaired; of these: 1303513 (2.92%) aligned 0 times 30101650 (67.33%) aligned exactly 1 time 13302515 (29.75%) aligned >1 times 97.08% overall alignment rate Time searching: 00:16:14 Overall time: 00:16:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 10215145 / 43404165 = 0.2353 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 @ Fri, 26 Jun 2020 09:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 26 Jun 2020 09:59:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:59:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:59:07: 1000000 INFO @ Fri, 26 Jun 2020 09:59:14: 2000000 INFO @ Fri, 26 Jun 2020 09:59:21: 3000000 INFO @ Fri, 26 Jun 2020 09:59:27: 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 @ Fri, 26 Jun 2020 09:59:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 26 Jun 2020 09:59:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:59:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:59:34: 5000000 INFO @ Fri, 26 Jun 2020 09:59:38: 1000000 INFO @ Fri, 26 Jun 2020 09:59:42: 6000000 INFO @ Fri, 26 Jun 2020 09:59:45: 2000000 INFO @ Fri, 26 Jun 2020 09:59:49: 7000000 INFO @ Fri, 26 Jun 2020 09:59:52: 3000000 INFO @ Fri, 26 Jun 2020 09:59:57: 8000000 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 @ Fri, 26 Jun 2020 10:00:00: 4000000 INFO @ Fri, 26 Jun 2020 10:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 26 Jun 2020 10:00:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:00:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:00:04: 9000000 INFO @ Fri, 26 Jun 2020 10:00:07: 5000000 INFO @ Fri, 26 Jun 2020 10:00:07: 1000000 INFO @ Fri, 26 Jun 2020 10:00:12: 10000000 INFO @ Fri, 26 Jun 2020 10:00:14: 6000000 INFO @ Fri, 26 Jun 2020 10:00:15: 2000000 INFO @ Fri, 26 Jun 2020 10:00:19: 11000000 INFO @ Fri, 26 Jun 2020 10:00:22: 3000000 INFO @ Fri, 26 Jun 2020 10:00:22: 7000000 INFO @ Fri, 26 Jun 2020 10:00:26: 12000000 INFO @ Fri, 26 Jun 2020 10:00:29: 4000000 INFO @ Fri, 26 Jun 2020 10:00:29: 8000000 INFO @ Fri, 26 Jun 2020 10:00:34: 13000000 INFO @ Fri, 26 Jun 2020 10:00:36: 5000000 INFO @ Fri, 26 Jun 2020 10:00:37: 9000000 INFO @ Fri, 26 Jun 2020 10:00:41: 14000000 INFO @ Fri, 26 Jun 2020 10:00:42: 6000000 INFO @ Fri, 26 Jun 2020 10:00:44: 10000000 INFO @ Fri, 26 Jun 2020 10:00:49: 15000000 INFO @ Fri, 26 Jun 2020 10:00:50: 7000000 INFO @ Fri, 26 Jun 2020 10:00:52: 11000000 INFO @ Fri, 26 Jun 2020 10:00:56: 16000000 INFO @ Fri, 26 Jun 2020 10:00:57: 8000000 INFO @ Fri, 26 Jun 2020 10:00:59: 12000000 INFO @ Fri, 26 Jun 2020 10:01:04: 17000000 INFO @ Fri, 26 Jun 2020 10:01:04: 9000000 INFO @ Fri, 26 Jun 2020 10:01:07: 13000000 INFO @ Fri, 26 Jun 2020 10:01:11: 18000000 INFO @ Fri, 26 Jun 2020 10:01:11: 10000000 INFO @ Fri, 26 Jun 2020 10:01:14: 14000000 INFO @ Fri, 26 Jun 2020 10:01:18: 11000000 INFO @ Fri, 26 Jun 2020 10:01:19: 19000000 INFO @ Fri, 26 Jun 2020 10:01:22: 15000000 INFO @ Fri, 26 Jun 2020 10:01:25: 12000000 INFO @ Fri, 26 Jun 2020 10:01:26: 20000000 INFO @ Fri, 26 Jun 2020 10:01:29: 16000000 INFO @ Fri, 26 Jun 2020 10:01:33: 13000000 INFO @ Fri, 26 Jun 2020 10:01:33: 21000000 INFO @ Fri, 26 Jun 2020 10:01:37: 17000000 INFO @ Fri, 26 Jun 2020 10:01:40: 14000000 INFO @ Fri, 26 Jun 2020 10:01:41: 22000000 INFO @ Fri, 26 Jun 2020 10:01:44: 18000000 INFO @ Fri, 26 Jun 2020 10:01:47: 15000000 INFO @ Fri, 26 Jun 2020 10:01:48: 23000000 INFO @ Fri, 26 Jun 2020 10:01:52: 19000000 INFO @ Fri, 26 Jun 2020 10:01:54: 16000000 INFO @ Fri, 26 Jun 2020 10:01:55: 24000000 INFO @ Fri, 26 Jun 2020 10:02:00: 20000000 INFO @ Fri, 26 Jun 2020 10:02:02: 17000000 INFO @ Fri, 26 Jun 2020 10:02:02: 25000000 INFO @ Fri, 26 Jun 2020 10:02:07: 21000000 INFO @ Fri, 26 Jun 2020 10:02:09: 18000000 INFO @ Fri, 26 Jun 2020 10:02:10: 26000000 INFO @ Fri, 26 Jun 2020 10:02:14: 22000000 INFO @ Fri, 26 Jun 2020 10:02:16: 19000000 INFO @ Fri, 26 Jun 2020 10:02:17: 27000000 INFO @ Fri, 26 Jun 2020 10:02:22: 23000000 INFO @ Fri, 26 Jun 2020 10:02:23: 20000000 INFO @ Fri, 26 Jun 2020 10:02:24: 28000000 INFO @ Fri, 26 Jun 2020 10:02:29: 24000000 INFO @ Fri, 26 Jun 2020 10:02:30: 21000000 INFO @ Fri, 26 Jun 2020 10:02:32: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:02:36: 25000000 INFO @ Fri, 26 Jun 2020 10:02:37: 22000000 INFO @ Fri, 26 Jun 2020 10:02:39: 30000000 INFO @ Fri, 26 Jun 2020 10:02:44: 26000000 INFO @ Fri, 26 Jun 2020 10:02:45: 23000000 INFO @ Fri, 26 Jun 2020 10:02:46: 31000000 INFO @ Fri, 26 Jun 2020 10:02:51: 27000000 INFO @ Fri, 26 Jun 2020 10:02:52: 24000000 INFO @ Fri, 26 Jun 2020 10:02:53: 32000000 INFO @ Fri, 26 Jun 2020 10:02:58: 28000000 INFO @ Fri, 26 Jun 2020 10:02:59: 25000000 INFO @ Fri, 26 Jun 2020 10:03:01: 33000000 INFO @ Fri, 26 Jun 2020 10:03:02: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:03:02: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:03:02: #1 total tags in treatment: 33189020 INFO @ Fri, 26 Jun 2020 10:03:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:03:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 10:03:03: #1 tags after filtering in treatment: 33189020 INFO @ Fri, 26 Jun 2020 10:03:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:03:03: #1 finished! INFO @ Fri, 26 Jun 2020 10:03:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:03:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:03:05: #2 number of paired peaks: 361 WARNING @ Fri, 26 Jun 2020 10:03:05: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 26 Jun 2020 10:03:05: start model_add_line... INFO @ Fri, 26 Jun 2020 10:03:05: start X-correlation... INFO @ Fri, 26 Jun 2020 10:03:05: end of X-cor INFO @ Fri, 26 Jun 2020 10:03:05: #2 finished! INFO @ Fri, 26 Jun 2020 10:03:05: #2 predicted fragment length is 137 bps INFO @ Fri, 26 Jun 2020 10:03:05: #2 alternative fragment length(s) may be 4,137 bps INFO @ Fri, 26 Jun 2020 10:03:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.05_model.r INFO @ Fri, 26 Jun 2020 10:03:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:03:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:03:06: 29000000 INFO @ Fri, 26 Jun 2020 10:03:06: 26000000 INFO @ Fri, 26 Jun 2020 10:03:13: 27000000 INFO @ Fri, 26 Jun 2020 10:03:13: 30000000 INFO @ Fri, 26 Jun 2020 10:03:20: 28000000 INFO @ Fri, 26 Jun 2020 10:03:20: 31000000 INFO @ Fri, 26 Jun 2020 10:03:27: 29000000 INFO @ Fri, 26 Jun 2020 10:03:27: 32000000 INFO @ Fri, 26 Jun 2020 10:03:34: 30000000 INFO @ Fri, 26 Jun 2020 10:03:35: 33000000 INFO @ Fri, 26 Jun 2020 10:03:37: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:03:37: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:03:37: #1 total tags in treatment: 33189020 INFO @ Fri, 26 Jun 2020 10:03:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:03:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 10:03:37: #1 tags after filtering in treatment: 33189020 INFO @ Fri, 26 Jun 2020 10:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:03:37: #1 finished! INFO @ Fri, 26 Jun 2020 10:03:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:03:39: #2 number of paired peaks: 361 WARNING @ Fri, 26 Jun 2020 10:03:39: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 26 Jun 2020 10:03:39: start model_add_line... INFO @ Fri, 26 Jun 2020 10:03:40: start X-correlation... INFO @ Fri, 26 Jun 2020 10:03:40: end of X-cor INFO @ Fri, 26 Jun 2020 10:03:40: #2 finished! INFO @ Fri, 26 Jun 2020 10:03:40: #2 predicted fragment length is 137 bps INFO @ Fri, 26 Jun 2020 10:03:40: #2 alternative fragment length(s) may be 4,137 bps INFO @ Fri, 26 Jun 2020 10:03:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.10_model.r INFO @ Fri, 26 Jun 2020 10:03:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:03:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:03:41: 31000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:03:47: 32000000 INFO @ Fri, 26 Jun 2020 10:03:54: 33000000 INFO @ Fri, 26 Jun 2020 10:03:56: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:03:56: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:03:56: #1 total tags in treatment: 33189020 INFO @ Fri, 26 Jun 2020 10:03:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:03:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 10:03:56: #1 tags after filtering in treatment: 33189020 INFO @ Fri, 26 Jun 2020 10:03:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:03:56: #1 finished! INFO @ Fri, 26 Jun 2020 10:03:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:03:59: #2 number of paired peaks: 361 WARNING @ Fri, 26 Jun 2020 10:03:59: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 26 Jun 2020 10:03:59: start model_add_line... INFO @ Fri, 26 Jun 2020 10:03:59: start X-correlation... INFO @ Fri, 26 Jun 2020 10:03:59: end of X-cor INFO @ Fri, 26 Jun 2020 10:03:59: #2 finished! INFO @ Fri, 26 Jun 2020 10:03:59: #2 predicted fragment length is 137 bps INFO @ Fri, 26 Jun 2020 10:03:59: #2 alternative fragment length(s) may be 4,137 bps INFO @ Fri, 26 Jun 2020 10:03:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.20_model.r INFO @ Fri, 26 Jun 2020 10:03:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:03:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:04:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:04:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:04:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:04:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.05_summits.bed INFO @ Fri, 26 Jun 2020 10:04:48: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12012 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:04:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:05:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:05:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:05:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:05:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.10_summits.bed INFO @ Fri, 26 Jun 2020 10:05:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8776 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:05:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:05:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:05:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX685464/SRX685464.20_summits.bed INFO @ Fri, 26 Jun 2020 10:05:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4935 records, 4 fields): 7 millis CompletedMACS2peakCalling