Job ID = 6366946 SRX = SRX2576647 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:14:46 prefetch.2.10.7: 1) Downloading 'SRR5272604'... 2020-06-15T23:14:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:16:39 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:16:40 prefetch.2.10.7: 'SRR5272604' is valid 2020-06-15T23:16:40 prefetch.2.10.7: 1) 'SRR5272604' was downloaded successfully Read 20063336 spots for SRR5272604/SRR5272604.sra Written 20063336 spots for SRR5272604/SRR5272604.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: 00:03:27 20063336 reads; of these: 20063336 (100.00%) were unpaired; of these: 271582 (1.35%) aligned 0 times 16302592 (81.26%) aligned exactly 1 time 3489162 (17.39%) aligned >1 times 98.65% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 3718115 / 19791754 = 0.1879 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 08:25:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.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 08:25:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:44: 1000000 INFO @ Tue, 16 Jun 2020 08:25:50: 2000000 INFO @ Tue, 16 Jun 2020 08:25:55: 3000000 INFO @ Tue, 16 Jun 2020 08:26:00: 4000000 INFO @ Tue, 16 Jun 2020 08:26:06: 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 08:26:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.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 08:26:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:11: 6000000 INFO @ Tue, 16 Jun 2020 08:26:15: 1000000 INFO @ Tue, 16 Jun 2020 08:26:17: 7000000 INFO @ Tue, 16 Jun 2020 08:26:20: 2000000 INFO @ Tue, 16 Jun 2020 08:26:22: 8000000 INFO @ Tue, 16 Jun 2020 08:26:26: 3000000 INFO @ Tue, 16 Jun 2020 08:26:29: 9000000 INFO @ Tue, 16 Jun 2020 08:26:31: 4000000 INFO @ Tue, 16 Jun 2020 08:26:35: 10000000 INFO @ Tue, 16 Jun 2020 08:26:37: 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 08:26:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.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 08:26:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:40: 11000000 INFO @ Tue, 16 Jun 2020 08:26:42: 6000000 INFO @ Tue, 16 Jun 2020 08:26:45: 1000000 INFO @ Tue, 16 Jun 2020 08:26:46: 12000000 INFO @ Tue, 16 Jun 2020 08:26:48: 7000000 INFO @ Tue, 16 Jun 2020 08:26:50: 2000000 INFO @ Tue, 16 Jun 2020 08:26:52: 13000000 INFO @ Tue, 16 Jun 2020 08:26:54: 8000000 INFO @ Tue, 16 Jun 2020 08:26:56: 3000000 INFO @ Tue, 16 Jun 2020 08:26:58: 14000000 INFO @ Tue, 16 Jun 2020 08:26:59: 9000000 INFO @ Tue, 16 Jun 2020 08:27:02: 4000000 INFO @ Tue, 16 Jun 2020 08:27:03: 15000000 INFO @ Tue, 16 Jun 2020 08:27:05: 10000000 INFO @ Tue, 16 Jun 2020 08:27:07: 5000000 INFO @ Tue, 16 Jun 2020 08:27:09: 16000000 INFO @ Tue, 16 Jun 2020 08:27:09: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:27:09: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:27:09: #1 total tags in treatment: 16073639 INFO @ Tue, 16 Jun 2020 08:27:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:09: #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 08:27:10: #1 tags after filtering in treatment: 16073639 INFO @ Tue, 16 Jun 2020 08:27:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:11: 11000000 INFO @ Tue, 16 Jun 2020 08:27:11: #2 number of paired peaks: 487 WARNING @ Tue, 16 Jun 2020 08:27:11: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:11: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 08:27:11: #2 alternative fragment length(s) may be 142 bps INFO @ Tue, 16 Jun 2020 08:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.05_model.r INFO @ Tue, 16 Jun 2020 08:27:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:13: 6000000 INFO @ Tue, 16 Jun 2020 08:27:16: 12000000 INFO @ Tue, 16 Jun 2020 08:27:19: 7000000 INFO @ Tue, 16 Jun 2020 08:27:22: 13000000 INFO @ Tue, 16 Jun 2020 08:27:24: 8000000 INFO @ Tue, 16 Jun 2020 08:27:28: 14000000 INFO @ Tue, 16 Jun 2020 08:27:30: 9000000 INFO @ Tue, 16 Jun 2020 08:27:33: 15000000 INFO @ Tue, 16 Jun 2020 08:27:36: 10000000 INFO @ Tue, 16 Jun 2020 08:27:39: 16000000 INFO @ Tue, 16 Jun 2020 08:27:39: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:27:39: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:27:39: #1 total tags in treatment: 16073639 INFO @ Tue, 16 Jun 2020 08:27:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:39: #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 08:27:40: #1 tags after filtering in treatment: 16073639 INFO @ Tue, 16 Jun 2020 08:27:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:41: #2 number of paired peaks: 487 WARNING @ Tue, 16 Jun 2020 08:27:41: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:41: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 08:27:41: #2 alternative fragment length(s) may be 142 bps INFO @ Tue, 16 Jun 2020 08:27:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.10_model.r INFO @ Tue, 16 Jun 2020 08:27:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:41: 11000000 INFO @ Tue, 16 Jun 2020 08:27:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:47: 12000000 INFO @ Tue, 16 Jun 2020 08:27:52: 13000000 INFO @ Tue, 16 Jun 2020 08:27:58: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2751 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:03: 15000000 INFO @ Tue, 16 Jun 2020 08:28:09: 16000000 INFO @ Tue, 16 Jun 2020 08:28:09: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:28:09: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:28:09: #1 total tags in treatment: 16073639 INFO @ Tue, 16 Jun 2020 08:28:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:09: #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 08:28:10: #1 tags after filtering in treatment: 16073639 INFO @ Tue, 16 Jun 2020 08:28:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:11: #2 number of paired peaks: 487 WARNING @ Tue, 16 Jun 2020 08:28:11: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:11: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 08:28:11: #2 alternative fragment length(s) may be 142 bps INFO @ Tue, 16 Jun 2020 08:28:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.20_model.r INFO @ Tue, 16 Jun 2020 08:28:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1986 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:28:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576647/SRX2576647.20_summits.bed INFO @ Tue, 16 Jun 2020 08:28:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1378 records, 4 fields): 3 millis CompletedMACS2peakCalling