Job ID = 6368914 SRX = SRX707298 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:42:57 prefetch.2.10.7: 1) Downloading 'SRR1582081'... 2020-06-16T00:42:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:48:46 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:48:46 prefetch.2.10.7: 1) 'SRR1582081' was downloaded successfully Read 34467748 spots for SRR1582081/SRR1582081.sra Written 34467748 spots for SRR1582081/SRR1582081.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: 00:08:28 34467748 reads; of these: 34467748 (100.00%) were unpaired; of these: 1560428 (4.53%) aligned 0 times 27725055 (80.44%) aligned exactly 1 time 5182265 (15.04%) aligned >1 times 95.47% overall alignment rate Time searching: 00:08:28 Overall time: 00:08:28 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] 7569210 / 32907320 = 0.2300 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 10:08:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.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 10:08:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:08:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:08:35: 1000000 INFO @ Tue, 16 Jun 2020 10:08:41: 2000000 INFO @ Tue, 16 Jun 2020 10:08:48: 3000000 INFO @ Tue, 16 Jun 2020 10:08:54: 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 @ Tue, 16 Jun 2020 10:08:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.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 10:08:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:08:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:09:01: 5000000 INFO @ Tue, 16 Jun 2020 10:09:05: 1000000 INFO @ Tue, 16 Jun 2020 10:09:08: 6000000 INFO @ Tue, 16 Jun 2020 10:09:12: 2000000 INFO @ Tue, 16 Jun 2020 10:09:15: 7000000 INFO @ Tue, 16 Jun 2020 10:09:18: 3000000 INFO @ Tue, 16 Jun 2020 10:09:22: 8000000 INFO @ Tue, 16 Jun 2020 10:09:25: 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 @ Tue, 16 Jun 2020 10:09:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.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 10:09:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:09:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:09:29: 9000000 INFO @ Tue, 16 Jun 2020 10:09:32: 5000000 INFO @ Tue, 16 Jun 2020 10:09:35: 10000000 INFO @ Tue, 16 Jun 2020 10:09:36: 1000000 INFO @ Tue, 16 Jun 2020 10:09:38: 6000000 INFO @ Tue, 16 Jun 2020 10:09:42: 11000000 INFO @ Tue, 16 Jun 2020 10:09:43: 2000000 INFO @ Tue, 16 Jun 2020 10:09:45: 7000000 INFO @ Tue, 16 Jun 2020 10:09:49: 12000000 INFO @ Tue, 16 Jun 2020 10:09:50: 3000000 INFO @ Tue, 16 Jun 2020 10:09:51: 8000000 INFO @ Tue, 16 Jun 2020 10:09:56: 13000000 INFO @ Tue, 16 Jun 2020 10:09:57: 4000000 INFO @ Tue, 16 Jun 2020 10:09:58: 9000000 INFO @ Tue, 16 Jun 2020 10:10:03: 14000000 INFO @ Tue, 16 Jun 2020 10:10:05: 10000000 INFO @ Tue, 16 Jun 2020 10:10:05: 5000000 INFO @ Tue, 16 Jun 2020 10:10:10: 15000000 INFO @ Tue, 16 Jun 2020 10:10:11: 11000000 INFO @ Tue, 16 Jun 2020 10:10:12: 6000000 INFO @ Tue, 16 Jun 2020 10:10:17: 16000000 INFO @ Tue, 16 Jun 2020 10:10:18: 12000000 INFO @ Tue, 16 Jun 2020 10:10:19: 7000000 INFO @ Tue, 16 Jun 2020 10:10:24: 17000000 INFO @ Tue, 16 Jun 2020 10:10:25: 13000000 INFO @ Tue, 16 Jun 2020 10:10:26: 8000000 INFO @ Tue, 16 Jun 2020 10:10:31: 18000000 INFO @ Tue, 16 Jun 2020 10:10:32: 14000000 INFO @ Tue, 16 Jun 2020 10:10:33: 9000000 INFO @ Tue, 16 Jun 2020 10:10:38: 19000000 INFO @ Tue, 16 Jun 2020 10:10:39: 15000000 INFO @ Tue, 16 Jun 2020 10:10:40: 10000000 INFO @ Tue, 16 Jun 2020 10:10:45: 20000000 INFO @ Tue, 16 Jun 2020 10:10:46: 16000000 INFO @ Tue, 16 Jun 2020 10:10:47: 11000000 INFO @ Tue, 16 Jun 2020 10:10:52: 21000000 INFO @ Tue, 16 Jun 2020 10:10:52: 17000000 INFO @ Tue, 16 Jun 2020 10:10:54: 12000000 INFO @ Tue, 16 Jun 2020 10:10:59: 18000000 INFO @ Tue, 16 Jun 2020 10:10:59: 22000000 INFO @ Tue, 16 Jun 2020 10:11:02: 13000000 INFO @ Tue, 16 Jun 2020 10:11:06: 19000000 INFO @ Tue, 16 Jun 2020 10:11:06: 23000000 INFO @ Tue, 16 Jun 2020 10:11:09: 14000000 INFO @ Tue, 16 Jun 2020 10:11:13: 20000000 INFO @ Tue, 16 Jun 2020 10:11:13: 24000000 INFO @ Tue, 16 Jun 2020 10:11:16: 15000000 INFO @ Tue, 16 Jun 2020 10:11:20: 21000000 INFO @ Tue, 16 Jun 2020 10:11:21: 25000000 INFO @ Tue, 16 Jun 2020 10:11:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:11:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:11:23: #1 total tags in treatment: 25338110 INFO @ Tue, 16 Jun 2020 10:11:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:11:23: #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 10:11:23: 16000000 INFO @ Tue, 16 Jun 2020 10:11:24: #1 tags after filtering in treatment: 25338110 INFO @ Tue, 16 Jun 2020 10:11:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:11:24: #1 finished! INFO @ Tue, 16 Jun 2020 10:11:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:11:25: #2 number of paired peaks: 253 WARNING @ Tue, 16 Jun 2020 10:11:25: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 16 Jun 2020 10:11:25: start model_add_line... INFO @ Tue, 16 Jun 2020 10:11:26: start X-correlation... INFO @ Tue, 16 Jun 2020 10:11:26: end of X-cor INFO @ Tue, 16 Jun 2020 10:11:26: #2 finished! INFO @ Tue, 16 Jun 2020 10:11:26: #2 predicted fragment length is 138 bps INFO @ Tue, 16 Jun 2020 10:11:26: #2 alternative fragment length(s) may be 2,85,104,138,167 bps INFO @ Tue, 16 Jun 2020 10:11:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.05_model.r INFO @ Tue, 16 Jun 2020 10:11:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:11:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:11:27: 22000000 INFO @ Tue, 16 Jun 2020 10:11:30: 17000000 INFO @ Tue, 16 Jun 2020 10:11:34: 23000000 INFO @ Tue, 16 Jun 2020 10:11:38: 18000000 INFO @ Tue, 16 Jun 2020 10:11:41: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:11:45: 19000000 INFO @ Tue, 16 Jun 2020 10:11:48: 25000000 INFO @ Tue, 16 Jun 2020 10:11:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:11:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:11:50: #1 total tags in treatment: 25338110 INFO @ Tue, 16 Jun 2020 10:11:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:11:50: #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 10:11:51: #1 tags after filtering in treatment: 25338110 INFO @ Tue, 16 Jun 2020 10:11:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:11:51: #1 finished! INFO @ Tue, 16 Jun 2020 10:11:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:11:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:11:52: 20000000 INFO @ Tue, 16 Jun 2020 10:11:53: #2 number of paired peaks: 253 WARNING @ Tue, 16 Jun 2020 10:11:53: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 16 Jun 2020 10:11:53: start model_add_line... INFO @ Tue, 16 Jun 2020 10:11:53: start X-correlation... INFO @ Tue, 16 Jun 2020 10:11:53: end of X-cor INFO @ Tue, 16 Jun 2020 10:11:53: #2 finished! INFO @ Tue, 16 Jun 2020 10:11:53: #2 predicted fragment length is 138 bps INFO @ Tue, 16 Jun 2020 10:11:53: #2 alternative fragment length(s) may be 2,85,104,138,167 bps INFO @ Tue, 16 Jun 2020 10:11:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.10_model.r INFO @ Tue, 16 Jun 2020 10:11:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:11:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:12:00: 21000000 INFO @ Tue, 16 Jun 2020 10:12:06: 22000000 INFO @ Tue, 16 Jun 2020 10:12:13: 23000000 INFO @ Tue, 16 Jun 2020 10:12:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:12:20: 24000000 INFO @ Tue, 16 Jun 2020 10:12:27: 25000000 INFO @ Tue, 16 Jun 2020 10:12:29: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:12:29: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:12:29: #1 total tags in treatment: 25338110 INFO @ Tue, 16 Jun 2020 10:12:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:12:29: #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 10:12:29: #1 tags after filtering in treatment: 25338110 INFO @ Tue, 16 Jun 2020 10:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:12:29: #1 finished! INFO @ Tue, 16 Jun 2020 10:12:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:12:31: #2 number of paired peaks: 253 WARNING @ Tue, 16 Jun 2020 10:12:31: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 16 Jun 2020 10:12:31: start model_add_line... INFO @ Tue, 16 Jun 2020 10:12:31: start X-correlation... INFO @ Tue, 16 Jun 2020 10:12:31: end of X-cor INFO @ Tue, 16 Jun 2020 10:12:31: #2 finished! INFO @ Tue, 16 Jun 2020 10:12:31: #2 predicted fragment length is 138 bps INFO @ Tue, 16 Jun 2020 10:12:31: #2 alternative fragment length(s) may be 2,85,104,138,167 bps INFO @ Tue, 16 Jun 2020 10:12:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.20_model.r INFO @ Tue, 16 Jun 2020 10:12:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:12:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:12:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:12:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:12:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.05_summits.bed INFO @ Tue, 16 Jun 2020 10:12:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2163 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:12:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:13:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:13:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:13:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.10_summits.bed INFO @ Tue, 16 Jun 2020 10:13:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1234 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:13:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:13:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:13:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:13:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX707298/SRX707298.20_summits.bed INFO @ Tue, 16 Jun 2020 10:13:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (567 records, 4 fields): 2 millis CompletedMACS2peakCalling