Job ID = 6366948 SRX = SRX2576649 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:09:01 prefetch.2.10.7: 1) Downloading 'SRR5272606'... 2020-06-15T23:09:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:11:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:11:07 prefetch.2.10.7: 1) 'SRR5272606' was downloaded successfully Read 19310034 spots for SRR5272606/SRR5272606.sra Written 19310034 spots for SRR5272606/SRR5272606.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: 00:04:29 19310034 reads; of these: 19310034 (100.00%) were unpaired; of these: 871718 (4.51%) aligned 0 times 15153867 (78.48%) aligned exactly 1 time 3284449 (17.01%) aligned >1 times 95.49% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:29 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] 4048833 / 18438316 = 0.2196 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 08:21:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.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 08:21:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:27: 1000000 INFO @ Tue, 16 Jun 2020 08:21:33: 2000000 INFO @ Tue, 16 Jun 2020 08:21:39: 3000000 INFO @ Tue, 16 Jun 2020 08:21:45: 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 08:21:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.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 08:21:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:52: 5000000 INFO @ Tue, 16 Jun 2020 08:21:57: 1000000 INFO @ Tue, 16 Jun 2020 08:21:58: 6000000 INFO @ Tue, 16 Jun 2020 08:22:04: 2000000 INFO @ Tue, 16 Jun 2020 08:22:05: 7000000 INFO @ Tue, 16 Jun 2020 08:22:11: 3000000 INFO @ Tue, 16 Jun 2020 08:22:12: 8000000 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 08:22:19: 4000000 INFO @ Tue, 16 Jun 2020 08:22:19: 9000000 INFO @ Tue, 16 Jun 2020 08:22:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.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 08:22:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:26: 5000000 INFO @ Tue, 16 Jun 2020 08:22:26: 10000000 INFO @ Tue, 16 Jun 2020 08:22:28: 1000000 INFO @ Tue, 16 Jun 2020 08:22:33: 6000000 INFO @ Tue, 16 Jun 2020 08:22:33: 11000000 INFO @ Tue, 16 Jun 2020 08:22:35: 2000000 INFO @ Tue, 16 Jun 2020 08:22:40: 7000000 INFO @ Tue, 16 Jun 2020 08:22:41: 12000000 INFO @ Tue, 16 Jun 2020 08:22:42: 3000000 INFO @ Tue, 16 Jun 2020 08:22:47: 8000000 INFO @ Tue, 16 Jun 2020 08:22:48: 13000000 INFO @ Tue, 16 Jun 2020 08:22:50: 4000000 INFO @ Tue, 16 Jun 2020 08:22:54: 9000000 INFO @ Tue, 16 Jun 2020 08:22:55: 14000000 INFO @ Tue, 16 Jun 2020 08:22:57: 5000000 INFO @ Tue, 16 Jun 2020 08:22:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:22:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:22:58: #1 total tags in treatment: 14389483 INFO @ Tue, 16 Jun 2020 08:22:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:58: #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 08:22:58: #1 tags after filtering in treatment: 14389483 INFO @ Tue, 16 Jun 2020 08:22:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:59: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 08:22:59: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:59: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:22:59: #2 alternative fragment length(s) may be 4,133 bps INFO @ Tue, 16 Jun 2020 08:22:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.05_model.r INFO @ Tue, 16 Jun 2020 08:22:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:01: 10000000 INFO @ Tue, 16 Jun 2020 08:23:04: 6000000 INFO @ Tue, 16 Jun 2020 08:23:08: 11000000 INFO @ Tue, 16 Jun 2020 08:23:12: 7000000 INFO @ Tue, 16 Jun 2020 08:23:15: 12000000 INFO @ Tue, 16 Jun 2020 08:23:19: 8000000 INFO @ Tue, 16 Jun 2020 08:23:22: 13000000 INFO @ Tue, 16 Jun 2020 08:23:27: 9000000 INFO @ Tue, 16 Jun 2020 08:23:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:29: 14000000 INFO @ Tue, 16 Jun 2020 08:23:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:23:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:23:32: #1 total tags in treatment: 14389483 INFO @ Tue, 16 Jun 2020 08:23:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:32: #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 08:23:32: #1 tags after filtering in treatment: 14389483 INFO @ Tue, 16 Jun 2020 08:23:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:34: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 08:23:34: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:34: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:23:34: #2 alternative fragment length(s) may be 4,133 bps INFO @ Tue, 16 Jun 2020 08:23:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.10_model.r INFO @ Tue, 16 Jun 2020 08:23:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:34: 10000000 INFO @ Tue, 16 Jun 2020 08:23:40: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:23:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.05_summits.bed INFO @ Tue, 16 Jun 2020 08:23:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1891 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:46: 12000000 INFO @ Tue, 16 Jun 2020 08:23:53: 13000000 INFO @ Tue, 16 Jun 2020 08:23:59: 14000000 INFO @ Tue, 16 Jun 2020 08:24:01: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:24:01: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:24:01: #1 total tags in treatment: 14389483 INFO @ Tue, 16 Jun 2020 08:24:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:01: #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 08:24:02: #1 tags after filtering in treatment: 14389483 INFO @ Tue, 16 Jun 2020 08:24:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:03: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 08:24:03: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:03: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:24:03: #2 alternative fragment length(s) may be 4,133 bps INFO @ Tue, 16 Jun 2020 08:24:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.20_model.r INFO @ Tue, 16 Jun 2020 08:24:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:24:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.10_summits.bed INFO @ Tue, 16 Jun 2020 08:24:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1321 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576649/SRX2576649.20_summits.bed INFO @ Tue, 16 Jun 2020 08:24:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (816 records, 4 fields): 3 millis CompletedMACS2peakCalling