Job ID = 6366073 SRX = SRX059245 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:32:21 prefetch.2.10.7: 1) Downloading 'SRR190685'... 2020-06-15T22:32:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:33:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:33:56 prefetch.2.10.7: 'SRR190685' is valid 2020-06-15T22:33:56 prefetch.2.10.7: 1) 'SRR190685' was downloaded successfully Read 25360297 spots for SRR190685/SRR190685.sra Written 25360297 spots for SRR190685/SRR190685.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: 00:04:16 25360297 reads; of these: 25360297 (100.00%) were unpaired; of these: 2316864 (9.14%) aligned 0 times 20435142 (80.58%) aligned exactly 1 time 2608291 (10.28%) aligned >1 times 90.86% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 7840981 / 23043433 = 0.3403 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 07:43:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.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 07:43:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:41: 1000000 INFO @ Tue, 16 Jun 2020 07:43:47: 2000000 INFO @ Tue, 16 Jun 2020 07:43:52: 3000000 INFO @ Tue, 16 Jun 2020 07:43:58: 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 07:44:04: 5000000 INFO @ Tue, 16 Jun 2020 07:44:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.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 07:44:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:10: 6000000 INFO @ Tue, 16 Jun 2020 07:44:11: 1000000 INFO @ Tue, 16 Jun 2020 07:44:17: 7000000 INFO @ Tue, 16 Jun 2020 07:44:18: 2000000 INFO @ Tue, 16 Jun 2020 07:44:23: 8000000 INFO @ Tue, 16 Jun 2020 07:44:24: 3000000 INFO @ Tue, 16 Jun 2020 07:44:29: 9000000 INFO @ Tue, 16 Jun 2020 07:44:30: 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 07:44:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.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 07:44:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:36: 10000000 INFO @ Tue, 16 Jun 2020 07:44:36: 5000000 INFO @ Tue, 16 Jun 2020 07:44:42: 1000000 INFO @ Tue, 16 Jun 2020 07:44:42: 11000000 INFO @ Tue, 16 Jun 2020 07:44:43: 6000000 INFO @ Tue, 16 Jun 2020 07:44:48: 2000000 INFO @ Tue, 16 Jun 2020 07:44:48: 12000000 INFO @ Tue, 16 Jun 2020 07:44:49: 7000000 INFO @ Tue, 16 Jun 2020 07:44:54: 13000000 INFO @ Tue, 16 Jun 2020 07:44:54: 3000000 INFO @ Tue, 16 Jun 2020 07:44:56: 8000000 INFO @ Tue, 16 Jun 2020 07:45:01: 14000000 INFO @ Tue, 16 Jun 2020 07:45:01: 4000000 INFO @ Tue, 16 Jun 2020 07:45:02: 9000000 INFO @ Tue, 16 Jun 2020 07:45:07: 15000000 INFO @ Tue, 16 Jun 2020 07:45:07: 5000000 INFO @ Tue, 16 Jun 2020 07:45:08: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:45:08: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:45:08: #1 total tags in treatment: 15202452 INFO @ Tue, 16 Jun 2020 07:45:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:08: #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 07:45:08: #1 tags after filtering in treatment: 15202452 INFO @ Tue, 16 Jun 2020 07:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:08: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:08: 10000000 INFO @ Tue, 16 Jun 2020 07:45:09: #2 number of paired peaks: 211 WARNING @ Tue, 16 Jun 2020 07:45:09: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:09: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:10: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:10: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:10: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:10: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 07:45:10: #2 alternative fragment length(s) may be 4,117,566 bps INFO @ Tue, 16 Jun 2020 07:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.05_model.r INFO @ Tue, 16 Jun 2020 07:45:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:45:13: 6000000 INFO @ Tue, 16 Jun 2020 07:45:15: 11000000 INFO @ Tue, 16 Jun 2020 07:45:20: 7000000 INFO @ Tue, 16 Jun 2020 07:45:21: 12000000 INFO @ Tue, 16 Jun 2020 07:45:26: 8000000 INFO @ Tue, 16 Jun 2020 07:45:27: 13000000 INFO @ Tue, 16 Jun 2020 07:45:32: 9000000 INFO @ Tue, 16 Jun 2020 07:45:33: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:45:38: 10000000 INFO @ Tue, 16 Jun 2020 07:45:39: 15000000 INFO @ Tue, 16 Jun 2020 07:45:40: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:45:40: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:45:40: #1 total tags in treatment: 15202452 INFO @ Tue, 16 Jun 2020 07:45:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:40: #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 07:45:40: #1 tags after filtering in treatment: 15202452 INFO @ Tue, 16 Jun 2020 07:45:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:40: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:41: #2 number of paired peaks: 211 WARNING @ Tue, 16 Jun 2020 07:45:41: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:41: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:41: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:41: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:41: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:41: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 07:45:41: #2 alternative fragment length(s) may be 4,117,566 bps INFO @ Tue, 16 Jun 2020 07:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.10_model.r INFO @ Tue, 16 Jun 2020 07:45:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:45:44: 11000000 INFO @ Tue, 16 Jun 2020 07:45:50: 12000000 INFO @ Tue, 16 Jun 2020 07:45:55: 13000000 INFO @ Tue, 16 Jun 2020 07:45:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.05_summits.bed INFO @ Tue, 16 Jun 2020 07:45:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7641 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:46:01: 14000000 INFO @ Tue, 16 Jun 2020 07:46:07: 15000000 INFO @ Tue, 16 Jun 2020 07:46:08: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:46:08: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:46:08: #1 total tags in treatment: 15202452 INFO @ Tue, 16 Jun 2020 07:46:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:46:08: #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 07:46:09: #1 tags after filtering in treatment: 15202452 INFO @ Tue, 16 Jun 2020 07:46:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:46:09: #1 finished! INFO @ Tue, 16 Jun 2020 07:46:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:46:10: #2 number of paired peaks: 211 WARNING @ Tue, 16 Jun 2020 07:46:10: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Tue, 16 Jun 2020 07:46:10: start model_add_line... INFO @ Tue, 16 Jun 2020 07:46:10: start X-correlation... INFO @ Tue, 16 Jun 2020 07:46:10: end of X-cor INFO @ Tue, 16 Jun 2020 07:46:10: #2 finished! INFO @ Tue, 16 Jun 2020 07:46:10: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 07:46:10: #2 alternative fragment length(s) may be 4,117,566 bps INFO @ Tue, 16 Jun 2020 07:46:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.20_model.r INFO @ Tue, 16 Jun 2020 07:46:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:46:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:46:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:46:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:46:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.10_summits.bed INFO @ Tue, 16 Jun 2020 07:46:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3586 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:46:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059245/SRX059245.20_summits.bed INFO @ Tue, 16 Jun 2020 07:47:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1067 records, 4 fields): 2 millis CompletedMACS2peakCalling