Job ID = 6368011 SRX = SRX466474 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:00:35 prefetch.2.10.7: 1) Downloading 'SRR1163540'... 2020-06-16T00:00:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:40 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:41 prefetch.2.10.7: 'SRR1163540' is valid 2020-06-16T00:01:41 prefetch.2.10.7: 1) 'SRR1163540' was downloaded successfully Read 16986480 spots for SRR1163540/SRR1163540.sra Written 16986480 spots for SRR1163540/SRR1163540.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: 00:03:46 16986480 reads; of these: 16986480 (100.00%) were unpaired; of these: 316046 (1.86%) aligned 0 times 15015250 (88.40%) aligned exactly 1 time 1655184 (9.74%) aligned >1 times 98.14% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 3292199 / 16670434 = 0.1975 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 09:10:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.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 09:10:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:29: 1000000 INFO @ Tue, 16 Jun 2020 09:10:33: 2000000 INFO @ Tue, 16 Jun 2020 09:10:38: 3000000 INFO @ Tue, 16 Jun 2020 09:10:42: 4000000 INFO @ Tue, 16 Jun 2020 09:10:47: 5000000 INFO @ Tue, 16 Jun 2020 09:10:52: 6000000 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 09:10:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.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 09:10:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:57: 7000000 INFO @ Tue, 16 Jun 2020 09:10:59: 1000000 INFO @ Tue, 16 Jun 2020 09:11:02: 8000000 INFO @ Tue, 16 Jun 2020 09:11:04: 2000000 INFO @ Tue, 16 Jun 2020 09:11:06: 9000000 INFO @ Tue, 16 Jun 2020 09:11:09: 3000000 INFO @ Tue, 16 Jun 2020 09:11:11: 10000000 INFO @ Tue, 16 Jun 2020 09:11:14: 4000000 INFO @ Tue, 16 Jun 2020 09:11:16: 11000000 INFO @ Tue, 16 Jun 2020 09:11:19: 5000000 INFO @ Tue, 16 Jun 2020 09:11:21: 12000000 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 09:11:24: 6000000 INFO @ Tue, 16 Jun 2020 09:11:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.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 09:11:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:26: 13000000 INFO @ Tue, 16 Jun 2020 09:11:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:11:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:11:28: #1 total tags in treatment: 13378235 INFO @ Tue, 16 Jun 2020 09:11:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:28: #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 09:11:28: #1 tags after filtering in treatment: 13378235 INFO @ Tue, 16 Jun 2020 09:11:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:29: 7000000 INFO @ Tue, 16 Jun 2020 09:11:29: #2 number of paired peaks: 644 WARNING @ Tue, 16 Jun 2020 09:11:29: Fewer paired peaks (644) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 644 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:29: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 09:11:29: #2 alternative fragment length(s) may be 3,137 bps INFO @ Tue, 16 Jun 2020 09:11:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.05_model.r INFO @ Tue, 16 Jun 2020 09:11:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:29: 1000000 INFO @ Tue, 16 Jun 2020 09:11:34: 8000000 INFO @ Tue, 16 Jun 2020 09:11:34: 2000000 INFO @ Tue, 16 Jun 2020 09:11:39: 9000000 INFO @ Tue, 16 Jun 2020 09:11:39: 3000000 INFO @ Tue, 16 Jun 2020 09:11:44: 10000000 INFO @ Tue, 16 Jun 2020 09:11:44: 4000000 INFO @ Tue, 16 Jun 2020 09:11:49: 11000000 INFO @ Tue, 16 Jun 2020 09:11:50: 5000000 INFO @ Tue, 16 Jun 2020 09:11:55: 12000000 INFO @ Tue, 16 Jun 2020 09:11:55: 6000000 INFO @ Tue, 16 Jun 2020 09:11:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:00: 13000000 INFO @ Tue, 16 Jun 2020 09:12:00: 7000000 INFO @ Tue, 16 Jun 2020 09:12:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:02: #1 total tags in treatment: 13378235 INFO @ Tue, 16 Jun 2020 09:12:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:02: #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 09:12:02: #1 tags after filtering in treatment: 13378235 INFO @ Tue, 16 Jun 2020 09:12:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:03: #2 number of paired peaks: 644 WARNING @ Tue, 16 Jun 2020 09:12:03: Fewer paired peaks (644) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 644 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:03: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 09:12:03: #2 alternative fragment length(s) may be 3,137 bps INFO @ Tue, 16 Jun 2020 09:12:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.10_model.r INFO @ Tue, 16 Jun 2020 09:12:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:05: 8000000 INFO @ Tue, 16 Jun 2020 09:12:10: 9000000 INFO @ Tue, 16 Jun 2020 09:12:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:13: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (11970 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:15: 10000000 INFO @ Tue, 16 Jun 2020 09:12:20: 11000000 INFO @ Tue, 16 Jun 2020 09:12:25: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:30: 13000000 INFO @ Tue, 16 Jun 2020 09:12:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:32: #1 total tags in treatment: 13378235 INFO @ Tue, 16 Jun 2020 09:12:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:32: #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 09:12:33: #1 tags after filtering in treatment: 13378235 INFO @ Tue, 16 Jun 2020 09:12:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:34: #2 number of paired peaks: 644 WARNING @ Tue, 16 Jun 2020 09:12:34: Fewer paired peaks (644) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 644 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:34: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 09:12:34: #2 alternative fragment length(s) may be 3,137 bps INFO @ Tue, 16 Jun 2020 09:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.20_model.r INFO @ Tue, 16 Jun 2020 09:12:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5633 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466474/SRX466474.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1617 records, 4 fields): 4 millis CompletedMACS2peakCalling