Job ID = 6507951 SRX = SRX495111 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:50:23 prefetch.2.10.7: 1) Downloading 'SRR1198643'... 2020-06-26T14:50:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:52:16 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:52:16 prefetch.2.10.7: 1) 'SRR1198643' was downloaded successfully Read 31048268 spots for SRR1198643/SRR1198643.sra Written 31048268 spots for SRR1198643/SRR1198643.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: 00:00:01 Multiseed full-index search: 00:06:47 31048268 reads; of these: 31048268 (100.00%) were unpaired; of these: 1432031 (4.61%) aligned 0 times 24452580 (78.76%) aligned exactly 1 time 5163657 (16.63%) aligned >1 times 95.39% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 8255304 / 29616237 = 0.2787 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 @ Sat, 27 Jun 2020 00:07:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.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 @ Sat, 27 Jun 2020 00:07:09: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:07:09: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:07:15: 1000000 INFO @ Sat, 27 Jun 2020 00:07:21: 2000000 INFO @ Sat, 27 Jun 2020 00:07:27: 3000000 INFO @ Sat, 27 Jun 2020 00:07:33: 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 @ Sat, 27 Jun 2020 00:07:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.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 @ Sat, 27 Jun 2020 00:07:37: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:07:37: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:07:39: 5000000 INFO @ Sat, 27 Jun 2020 00:07:44: 1000000 INFO @ Sat, 27 Jun 2020 00:07:45: 6000000 INFO @ Sat, 27 Jun 2020 00:07:51: 2000000 INFO @ Sat, 27 Jun 2020 00:07:52: 7000000 INFO @ Sat, 27 Jun 2020 00:07:58: 8000000 INFO @ Sat, 27 Jun 2020 00:07:59: 3000000 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 @ Sat, 27 Jun 2020 00:08:04: 9000000 INFO @ Sat, 27 Jun 2020 00:08:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.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 @ Sat, 27 Jun 2020 00:08:05: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:08:05: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:08:09: 4000000 INFO @ Sat, 27 Jun 2020 00:08:11: 10000000 INFO @ Sat, 27 Jun 2020 00:08:12: 1000000 INFO @ Sat, 27 Jun 2020 00:08:18: 11000000 INFO @ Sat, 27 Jun 2020 00:08:19: 2000000 INFO @ Sat, 27 Jun 2020 00:08:21: 5000000 INFO @ Sat, 27 Jun 2020 00:08:24: 12000000 INFO @ Sat, 27 Jun 2020 00:08:25: 3000000 INFO @ Sat, 27 Jun 2020 00:08:29: 6000000 INFO @ Sat, 27 Jun 2020 00:08:31: 13000000 INFO @ Sat, 27 Jun 2020 00:08:32: 4000000 INFO @ Sat, 27 Jun 2020 00:08:38: 7000000 INFO @ Sat, 27 Jun 2020 00:08:38: 14000000 INFO @ Sat, 27 Jun 2020 00:08:39: 5000000 INFO @ Sat, 27 Jun 2020 00:08:45: 8000000 INFO @ Sat, 27 Jun 2020 00:08:45: 15000000 INFO @ Sat, 27 Jun 2020 00:08:46: 6000000 INFO @ Sat, 27 Jun 2020 00:08:52: 16000000 INFO @ Sat, 27 Jun 2020 00:08:52: 7000000 INFO @ Sat, 27 Jun 2020 00:08:53: 9000000 INFO @ Sat, 27 Jun 2020 00:08:59: 17000000 INFO @ Sat, 27 Jun 2020 00:08:59: 8000000 INFO @ Sat, 27 Jun 2020 00:09:00: 10000000 INFO @ Sat, 27 Jun 2020 00:09:05: 18000000 INFO @ Sat, 27 Jun 2020 00:09:06: 9000000 INFO @ Sat, 27 Jun 2020 00:09:08: 11000000 INFO @ Sat, 27 Jun 2020 00:09:12: 19000000 INFO @ Sat, 27 Jun 2020 00:09:13: 10000000 INFO @ Sat, 27 Jun 2020 00:09:15: 12000000 INFO @ Sat, 27 Jun 2020 00:09:19: 20000000 INFO @ Sat, 27 Jun 2020 00:09:19: 11000000 INFO @ Sat, 27 Jun 2020 00:09:23: 13000000 INFO @ Sat, 27 Jun 2020 00:09:26: 12000000 INFO @ Sat, 27 Jun 2020 00:09:26: 21000000 INFO @ Sat, 27 Jun 2020 00:09:29: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:09:29: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:09:29: #1 total tags in treatment: 21360933 INFO @ Sat, 27 Jun 2020 00:09:29: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:09:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:09:29: #1 tags after filtering in treatment: 21360933 INFO @ Sat, 27 Jun 2020 00:09:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:09:29: #1 finished! INFO @ Sat, 27 Jun 2020 00:09:29: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:09:30: 14000000 INFO @ Sat, 27 Jun 2020 00:09:31: #2 number of paired peaks: 390 WARNING @ Sat, 27 Jun 2020 00:09:31: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Sat, 27 Jun 2020 00:09:31: start model_add_line... INFO @ Sat, 27 Jun 2020 00:09:31: start X-correlation... INFO @ Sat, 27 Jun 2020 00:09:31: end of X-cor INFO @ Sat, 27 Jun 2020 00:09:31: #2 finished! INFO @ Sat, 27 Jun 2020 00:09:31: #2 predicted fragment length is 151 bps INFO @ Sat, 27 Jun 2020 00:09:31: #2 alternative fragment length(s) may be 4,151 bps INFO @ Sat, 27 Jun 2020 00:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.05_model.r INFO @ Sat, 27 Jun 2020 00:09:31: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:09:33: 13000000 INFO @ Sat, 27 Jun 2020 00:09:37: 15000000 INFO @ Sat, 27 Jun 2020 00:09:39: 14000000 INFO @ Sat, 27 Jun 2020 00:09:43: 16000000 INFO @ Sat, 27 Jun 2020 00:09:46: 15000000 INFO @ Sat, 27 Jun 2020 00:09:50: 17000000 INFO @ Sat, 27 Jun 2020 00:09:53: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:09:58: 18000000 INFO @ Sat, 27 Jun 2020 00:09:59: 17000000 INFO @ Sat, 27 Jun 2020 00:10:04: 19000000 INFO @ Sat, 27 Jun 2020 00:10:06: 18000000 INFO @ Sat, 27 Jun 2020 00:10:10: 20000000 INFO @ Sat, 27 Jun 2020 00:10:12: 19000000 INFO @ Sat, 27 Jun 2020 00:10:15: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:10:17: 21000000 INFO @ Sat, 27 Jun 2020 00:10:19: 20000000 INFO @ Sat, 27 Jun 2020 00:10:19: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:10:19: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:10:19: #1 total tags in treatment: 21360933 INFO @ Sat, 27 Jun 2020 00:10:19: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:10:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:10:19: #1 tags after filtering in treatment: 21360933 INFO @ Sat, 27 Jun 2020 00:10:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:10:19: #1 finished! INFO @ Sat, 27 Jun 2020 00:10:19: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:10:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:10:21: #2 number of paired peaks: 390 WARNING @ Sat, 27 Jun 2020 00:10:21: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Sat, 27 Jun 2020 00:10:21: start model_add_line... INFO @ Sat, 27 Jun 2020 00:10:21: start X-correlation... INFO @ Sat, 27 Jun 2020 00:10:21: end of X-cor INFO @ Sat, 27 Jun 2020 00:10:21: #2 finished! INFO @ Sat, 27 Jun 2020 00:10:21: #2 predicted fragment length is 151 bps INFO @ Sat, 27 Jun 2020 00:10:21: #2 alternative fragment length(s) may be 4,151 bps INFO @ Sat, 27 Jun 2020 00:10:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.10_model.r INFO @ Sat, 27 Jun 2020 00:10:21: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:10:25: 21000000 INFO @ Sat, 27 Jun 2020 00:10:27: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:10:27: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:10:27: #1 total tags in treatment: 21360933 INFO @ Sat, 27 Jun 2020 00:10:27: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:10:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:10:27: #1 tags after filtering in treatment: 21360933 INFO @ Sat, 27 Jun 2020 00:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:10:27: #1 finished! INFO @ Sat, 27 Jun 2020 00:10:27: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:10:29: #2 number of paired peaks: 390 WARNING @ Sat, 27 Jun 2020 00:10:29: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Sat, 27 Jun 2020 00:10:29: start model_add_line... INFO @ Sat, 27 Jun 2020 00:10:29: start X-correlation... INFO @ Sat, 27 Jun 2020 00:10:29: end of X-cor INFO @ Sat, 27 Jun 2020 00:10:29: #2 finished! INFO @ Sat, 27 Jun 2020 00:10:29: #2 predicted fragment length is 151 bps INFO @ Sat, 27 Jun 2020 00:10:29: #2 alternative fragment length(s) may be 4,151 bps INFO @ Sat, 27 Jun 2020 00:10:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.20_model.r INFO @ Sat, 27 Jun 2020 00:10:29: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:10:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:10:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:10:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:10:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.05_summits.bed INFO @ Sat, 27 Jun 2020 00:10:39: Done! pass1 - making usageList (7 chroms): 22 millis pass2 - checking and writing primary data (6339 records, 4 fields): 61 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:11:08: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:11:18: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.10_summits.bed INFO @ Sat, 27 Jun 2020 00:11:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4486 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:11:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:11:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495111/SRX495111.20_summits.bed INFO @ Sat, 27 Jun 2020 00:11:43: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2479 records, 4 fields): 19 millis CompletedMACS2peakCalling