Job ID = 6368166 SRX = SRX494850 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:58:35 prefetch.2.10.7: 1) Downloading 'SRR1198382'... 2020-06-15T23:58:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:09 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:09 prefetch.2.10.7: 1) 'SRR1198382' was downloaded successfully Read 18128454 spots for SRR1198382/SRR1198382.sra Written 18128454 spots for SRR1198382/SRR1198382.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: 00:03:14 18128454 reads; of these: 18128454 (100.00%) were unpaired; of these: 282825 (1.56%) aligned 0 times 15395193 (84.92%) aligned exactly 1 time 2450436 (13.52%) aligned >1 times 98.44% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3709734 / 17845629 = 0.2079 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 09:09:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.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 09:09:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:28: 1000000 INFO @ Tue, 16 Jun 2020 09:09:33: 2000000 INFO @ Tue, 16 Jun 2020 09:09:39: 3000000 INFO @ Tue, 16 Jun 2020 09:09:45: 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 09:09:51: 5000000 INFO @ Tue, 16 Jun 2020 09:09:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.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 09:09:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:58: 6000000 INFO @ Tue, 16 Jun 2020 09:10:00: 1000000 INFO @ Tue, 16 Jun 2020 09:10:05: 7000000 INFO @ Tue, 16 Jun 2020 09:10:08: 2000000 INFO @ Tue, 16 Jun 2020 09:10:12: 8000000 INFO @ Tue, 16 Jun 2020 09:10:15: 3000000 INFO @ Tue, 16 Jun 2020 09:10:20: 9000000 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 09:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.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 09:10:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:23: 4000000 INFO @ Tue, 16 Jun 2020 09:10:27: 10000000 INFO @ Tue, 16 Jun 2020 09:10:29: 1000000 INFO @ Tue, 16 Jun 2020 09:10:31: 5000000 INFO @ Tue, 16 Jun 2020 09:10:34: 11000000 INFO @ Tue, 16 Jun 2020 09:10:36: 2000000 INFO @ Tue, 16 Jun 2020 09:10:39: 6000000 INFO @ Tue, 16 Jun 2020 09:10:42: 12000000 INFO @ Tue, 16 Jun 2020 09:10:44: 3000000 INFO @ Tue, 16 Jun 2020 09:10:46: 7000000 INFO @ Tue, 16 Jun 2020 09:10:49: 13000000 INFO @ Tue, 16 Jun 2020 09:10:51: 4000000 INFO @ Tue, 16 Jun 2020 09:10:54: 8000000 INFO @ Tue, 16 Jun 2020 09:10:56: 14000000 INFO @ Tue, 16 Jun 2020 09:10:57: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:10:57: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:10:57: #1 total tags in treatment: 14135895 INFO @ Tue, 16 Jun 2020 09:10:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:57: #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 09:10:57: #1 tags after filtering in treatment: 14135895 INFO @ Tue, 16 Jun 2020 09:10:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:58: 5000000 INFO @ Tue, 16 Jun 2020 09:10:58: #2 number of paired peaks: 394 WARNING @ Tue, 16 Jun 2020 09:10:58: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:58: #2 predicted fragment length is 191 bps INFO @ Tue, 16 Jun 2020 09:10:58: #2 alternative fragment length(s) may be 3,167,191 bps INFO @ Tue, 16 Jun 2020 09:10:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.05_model.r INFO @ Tue, 16 Jun 2020 09:10:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:01: 9000000 INFO @ Tue, 16 Jun 2020 09:11:05: 6000000 INFO @ Tue, 16 Jun 2020 09:11:09: 10000000 INFO @ Tue, 16 Jun 2020 09:11:12: 7000000 INFO @ Tue, 16 Jun 2020 09:11:16: 11000000 INFO @ Tue, 16 Jun 2020 09:11:19: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:11:24: 12000000 INFO @ Tue, 16 Jun 2020 09:11:27: 9000000 INFO @ Tue, 16 Jun 2020 09:11:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:32: 13000000 INFO @ Tue, 16 Jun 2020 09:11:34: 10000000 INFO @ Tue, 16 Jun 2020 09:11:39: 14000000 INFO @ Tue, 16 Jun 2020 09:11:40: 11000000 INFO @ Tue, 16 Jun 2020 09:11:40: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:11:40: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:11:40: #1 total tags in treatment: 14135895 INFO @ Tue, 16 Jun 2020 09:11:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:40: #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 09:11:41: #1 tags after filtering in treatment: 14135895 INFO @ Tue, 16 Jun 2020 09:11:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:42: #2 number of paired peaks: 394 WARNING @ Tue, 16 Jun 2020 09:11:42: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:42: #2 predicted fragment length is 191 bps INFO @ Tue, 16 Jun 2020 09:11:42: #2 alternative fragment length(s) may be 3,167,191 bps INFO @ Tue, 16 Jun 2020 09:11:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.10_model.r INFO @ Tue, 16 Jun 2020 09:11:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7065 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:11:47: 12000000 INFO @ Tue, 16 Jun 2020 09:11:53: 13000000 INFO @ Tue, 16 Jun 2020 09:11:59: 14000000 INFO @ Tue, 16 Jun 2020 09:12:00: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:00: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:00: #1 total tags in treatment: 14135895 INFO @ Tue, 16 Jun 2020 09:12:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:00: #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 09:12:00: #1 tags after filtering in treatment: 14135895 INFO @ Tue, 16 Jun 2020 09:12:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:01: #2 number of paired peaks: 394 WARNING @ Tue, 16 Jun 2020 09:12:01: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:01: #2 predicted fragment length is 191 bps INFO @ Tue, 16 Jun 2020 09:12:01: #2 alternative fragment length(s) may be 3,167,191 bps INFO @ Tue, 16 Jun 2020 09:12:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.20_model.r INFO @ Tue, 16 Jun 2020 09:12:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2579 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494850/SRX494850.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (412 records, 4 fields): 1 millis CompletedMACS2peakCalling