Job ID = 6366516 SRX = SRX1674096 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:43:07 prefetch.2.10.7: 1) Downloading 'SRR3320142'... 2020-06-15T22:43:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:47:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:47:16 prefetch.2.10.7: 1) 'SRR3320142' was downloaded successfully Read 57969022 spots for SRR3320142/SRR3320142.sra Written 57969022 spots for SRR3320142/SRR3320142.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: 00:09:06 57969022 reads; of these: 57969022 (100.00%) were unpaired; of these: 22456725 (38.74%) aligned 0 times 30036562 (51.81%) aligned exactly 1 time 5475735 (9.45%) aligned >1 times 61.26% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 14986923 / 35512297 = 0.4220 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 @ Tue, 16 Jun 2020 08:05:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:05:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:05: 1000000 INFO @ Tue, 16 Jun 2020 08:06:11: 2000000 INFO @ Tue, 16 Jun 2020 08:06:16: 3000000 INFO @ Tue, 16 Jun 2020 08:06:22: 4000000 INFO @ Tue, 16 Jun 2020 08:06:27: 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 @ Tue, 16 Jun 2020 08:06:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:06:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:33: 6000000 INFO @ Tue, 16 Jun 2020 08:06:35: 1000000 INFO @ Tue, 16 Jun 2020 08:06:38: 7000000 INFO @ Tue, 16 Jun 2020 08:06:40: 2000000 INFO @ Tue, 16 Jun 2020 08:06:43: 8000000 INFO @ Tue, 16 Jun 2020 08:06:45: 3000000 INFO @ Tue, 16 Jun 2020 08:06:49: 9000000 INFO @ Tue, 16 Jun 2020 08:06:50: 4000000 INFO @ Tue, 16 Jun 2020 08:06:55: 10000000 INFO @ Tue, 16 Jun 2020 08:06:55: 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 @ Tue, 16 Jun 2020 08:06:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:06:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:00: 6000000 INFO @ Tue, 16 Jun 2020 08:07:01: 11000000 INFO @ Tue, 16 Jun 2020 08:07:05: 1000000 INFO @ Tue, 16 Jun 2020 08:07:05: 7000000 INFO @ Tue, 16 Jun 2020 08:07:07: 12000000 INFO @ Tue, 16 Jun 2020 08:07:10: 2000000 INFO @ Tue, 16 Jun 2020 08:07:11: 8000000 INFO @ Tue, 16 Jun 2020 08:07:12: 13000000 INFO @ Tue, 16 Jun 2020 08:07:15: 3000000 INFO @ Tue, 16 Jun 2020 08:07:16: 9000000 INFO @ Tue, 16 Jun 2020 08:07:18: 14000000 INFO @ Tue, 16 Jun 2020 08:07:20: 4000000 INFO @ Tue, 16 Jun 2020 08:07:21: 10000000 INFO @ Tue, 16 Jun 2020 08:07:24: 15000000 INFO @ Tue, 16 Jun 2020 08:07:26: 5000000 INFO @ Tue, 16 Jun 2020 08:07:27: 11000000 INFO @ Tue, 16 Jun 2020 08:07:30: 16000000 INFO @ Tue, 16 Jun 2020 08:07:31: 6000000 INFO @ Tue, 16 Jun 2020 08:07:32: 12000000 INFO @ Tue, 16 Jun 2020 08:07:36: 17000000 INFO @ Tue, 16 Jun 2020 08:07:36: 7000000 INFO @ Tue, 16 Jun 2020 08:07:37: 13000000 INFO @ Tue, 16 Jun 2020 08:07:41: 8000000 INFO @ Tue, 16 Jun 2020 08:07:42: 18000000 INFO @ Tue, 16 Jun 2020 08:07:43: 14000000 INFO @ Tue, 16 Jun 2020 08:07:47: 9000000 INFO @ Tue, 16 Jun 2020 08:07:47: 19000000 INFO @ Tue, 16 Jun 2020 08:07:48: 15000000 INFO @ Tue, 16 Jun 2020 08:07:52: 10000000 INFO @ Tue, 16 Jun 2020 08:07:53: 20000000 INFO @ Tue, 16 Jun 2020 08:07:53: 16000000 INFO @ Tue, 16 Jun 2020 08:07:56: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:56: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:56: #1 total tags in treatment: 20525374 INFO @ Tue, 16 Jun 2020 08:07:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:07:57: #1 tags after filtering in treatment: 20525374 INFO @ Tue, 16 Jun 2020 08:07:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:57: 11000000 INFO @ Tue, 16 Jun 2020 08:07:58: #2 number of paired peaks: 784 WARNING @ Tue, 16 Jun 2020 08:07:58: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:58: #2 predicted fragment length is 227 bps INFO @ Tue, 16 Jun 2020 08:07:58: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 16 Jun 2020 08:07:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.05_model.r INFO @ Tue, 16 Jun 2020 08:07:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:58: 17000000 INFO @ Tue, 16 Jun 2020 08:08:02: 12000000 INFO @ Tue, 16 Jun 2020 08:08:04: 18000000 INFO @ Tue, 16 Jun 2020 08:08:08: 13000000 INFO @ Tue, 16 Jun 2020 08:08:09: 19000000 INFO @ Tue, 16 Jun 2020 08:08:13: 14000000 INFO @ Tue, 16 Jun 2020 08:08:14: 20000000 INFO @ Tue, 16 Jun 2020 08:08:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:08:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:08:17: #1 total tags in treatment: 20525374 INFO @ Tue, 16 Jun 2020 08:08:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:08:17: #1 tags after filtering in treatment: 20525374 INFO @ Tue, 16 Jun 2020 08:08:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:18: 15000000 INFO @ Tue, 16 Jun 2020 08:08:18: #2 number of paired peaks: 784 WARNING @ Tue, 16 Jun 2020 08:08:18: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:18: #2 predicted fragment length is 227 bps INFO @ Tue, 16 Jun 2020 08:08:18: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 16 Jun 2020 08:08:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.10_model.r INFO @ Tue, 16 Jun 2020 08:08:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:23: 16000000 INFO @ Tue, 16 Jun 2020 08:08:28: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:32: 18000000 INFO @ Tue, 16 Jun 2020 08:08:37: 19000000 INFO @ Tue, 16 Jun 2020 08:08:42: 20000000 INFO @ Tue, 16 Jun 2020 08:08:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:08:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:08:44: #1 total tags in treatment: 20525374 INFO @ Tue, 16 Jun 2020 08:08:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:08:45: #1 tags after filtering in treatment: 20525374 INFO @ Tue, 16 Jun 2020 08:08:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:46: #2 number of paired peaks: 784 WARNING @ Tue, 16 Jun 2020 08:08:46: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:46: #2 predicted fragment length is 227 bps INFO @ Tue, 16 Jun 2020 08:08:46: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 16 Jun 2020 08:08:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.20_model.r INFO @ Tue, 16 Jun 2020 08:08:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:09:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.05_summits.bed INFO @ Tue, 16 Jun 2020 08:09:10: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (16840 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:09:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.10_summits.bed INFO @ Tue, 16 Jun 2020 08:09:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9987 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:09:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674096/SRX1674096.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5321 records, 4 fields): 6 millis CompletedMACS2peakCalling