Job ID = 6366738 SRX = SRX2228891 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:03:23 prefetch.2.10.7: 1) Downloading 'SRR4380347'... 2020-06-15T23:03:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:04:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:04:04 prefetch.2.10.7: 'SRR4380347' is valid 2020-06-15T23:04:04 prefetch.2.10.7: 1) 'SRR4380347' was downloaded successfully 2020-06-15T23:04:04 prefetch.2.10.7: 'SRR4380347' has 0 unresolved dependencies Read 15404718 spots for SRR4380347/SRR4380347.sra Written 15404718 spots for SRR4380347/SRR4380347.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 15404718 reads; of these: 15404718 (100.00%) were unpaired; of these: 1179855 (7.66%) aligned 0 times 11951966 (77.59%) aligned exactly 1 time 2272897 (14.75%) aligned >1 times 92.34% 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] 2200160 / 14224863 = 0.1547 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 08:12:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.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 08:12:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:11: 1000000 INFO @ Tue, 16 Jun 2020 08:12:16: 2000000 INFO @ Tue, 16 Jun 2020 08:12:21: 3000000 INFO @ Tue, 16 Jun 2020 08:12:27: 4000000 INFO @ Tue, 16 Jun 2020 08:12:32: 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 08:12:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.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 08:12:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:37: 6000000 INFO @ Tue, 16 Jun 2020 08:12:41: 1000000 INFO @ Tue, 16 Jun 2020 08:12:43: 7000000 INFO @ Tue, 16 Jun 2020 08:12:47: 2000000 INFO @ Tue, 16 Jun 2020 08:12:49: 8000000 INFO @ Tue, 16 Jun 2020 08:12:52: 3000000 INFO @ Tue, 16 Jun 2020 08:12:54: 9000000 INFO @ Tue, 16 Jun 2020 08:12:58: 4000000 INFO @ Tue, 16 Jun 2020 08:13:00: 10000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 08:13:04: 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 08:13:05: 11000000 INFO @ Tue, 16 Jun 2020 08:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.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 08:13:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:09: 6000000 INFO @ Tue, 16 Jun 2020 08:13:11: 12000000 INFO @ Tue, 16 Jun 2020 08:13:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:13:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:13:11: #1 total tags in treatment: 12024703 INFO @ Tue, 16 Jun 2020 08:13:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:11: #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 08:13:11: #1 tags after filtering in treatment: 12024703 INFO @ Tue, 16 Jun 2020 08:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:12: 1000000 INFO @ Tue, 16 Jun 2020 08:13:12: #2 number of paired peaks: 556 WARNING @ Tue, 16 Jun 2020 08:13:12: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:12: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:13:12: #2 alternative fragment length(s) may be 128,133 bps INFO @ Tue, 16 Jun 2020 08:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.05_model.r INFO @ Tue, 16 Jun 2020 08:13:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:15: 7000000 INFO @ Tue, 16 Jun 2020 08:13:19: 2000000 INFO @ Tue, 16 Jun 2020 08:13:21: 8000000 INFO @ Tue, 16 Jun 2020 08:13:25: 3000000 INFO @ Tue, 16 Jun 2020 08:13:27: 9000000 INFO @ Tue, 16 Jun 2020 08:13:32: 4000000 INFO @ Tue, 16 Jun 2020 08:13:33: 10000000 INFO @ Tue, 16 Jun 2020 08:13:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:38: 5000000 INFO @ Tue, 16 Jun 2020 08:13:39: 11000000 INFO @ Tue, 16 Jun 2020 08:13:44: 12000000 INFO @ Tue, 16 Jun 2020 08:13:44: 6000000 INFO @ Tue, 16 Jun 2020 08:13:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:13:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:13:45: #1 total tags in treatment: 12024703 INFO @ Tue, 16 Jun 2020 08:13:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:45: #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 08:13:45: #1 tags after filtering in treatment: 12024703 INFO @ Tue, 16 Jun 2020 08:13:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:46: #2 number of paired peaks: 556 WARNING @ Tue, 16 Jun 2020 08:13:46: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:46: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:13:46: #2 alternative fragment length(s) may be 128,133 bps INFO @ Tue, 16 Jun 2020 08:13:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.10_model.r INFO @ Tue, 16 Jun 2020 08:13:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:51: 7000000 INFO @ Tue, 16 Jun 2020 08:13:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.05_summits.bed INFO @ Tue, 16 Jun 2020 08:13:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1868 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:13:57: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:03: 9000000 INFO @ Tue, 16 Jun 2020 08:14:09: 10000000 INFO @ Tue, 16 Jun 2020 08:14:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:15: 11000000 INFO @ Tue, 16 Jun 2020 08:14:20: 12000000 INFO @ Tue, 16 Jun 2020 08:14:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:21: #1 total tags in treatment: 12024703 INFO @ Tue, 16 Jun 2020 08:14:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:21: #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 08:14:21: #1 tags after filtering in treatment: 12024703 INFO @ Tue, 16 Jun 2020 08:14:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:22: #2 number of paired peaks: 556 WARNING @ Tue, 16 Jun 2020 08:14:22: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:22: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:14:22: #2 alternative fragment length(s) may be 128,133 bps INFO @ Tue, 16 Jun 2020 08:14:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.20_model.r INFO @ Tue, 16 Jun 2020 08:14:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.10_summits.bed INFO @ Tue, 16 Jun 2020 08:14:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1189 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:14:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228891/SRX2228891.20_summits.bed INFO @ Tue, 16 Jun 2020 08:14:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (728 records, 4 fields): 2 millis CompletedMACS2peakCalling