Job ID = 6366923 SRX = SRX2576626 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:24:05 prefetch.2.10.7: 1) Downloading 'SRR5272583'... 2020-06-15T23:24:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:25:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:25:03 prefetch.2.10.7: 'SRR5272583' is valid 2020-06-15T23:25:03 prefetch.2.10.7: 1) 'SRR5272583' was downloaded successfully Read 17606297 spots for SRR5272583/SRR5272583.sra Written 17606297 spots for SRR5272583/SRR5272583.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: 00:02:51 17606297 reads; of these: 17606297 (100.00%) were unpaired; of these: 655022 (3.72%) aligned 0 times 13986292 (79.44%) aligned exactly 1 time 2964983 (16.84%) aligned >1 times 96.28% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 2562384 / 16951275 = 0.1512 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 08:32:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.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 08:32:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:47: 1000000 INFO @ Tue, 16 Jun 2020 08:32:53: 2000000 INFO @ Tue, 16 Jun 2020 08:32:59: 3000000 INFO @ Tue, 16 Jun 2020 08:33:05: 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 08:33:10: 5000000 INFO @ Tue, 16 Jun 2020 08:33:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.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 08:33:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:17: 6000000 INFO @ Tue, 16 Jun 2020 08:33:18: 1000000 INFO @ Tue, 16 Jun 2020 08:33:23: 7000000 INFO @ Tue, 16 Jun 2020 08:33:24: 2000000 INFO @ Tue, 16 Jun 2020 08:33:29: 8000000 INFO @ Tue, 16 Jun 2020 08:33:31: 3000000 INFO @ Tue, 16 Jun 2020 08:33:36: 9000000 INFO @ Tue, 16 Jun 2020 08:33:37: 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 08:33:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.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 08:33:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:42: 10000000 INFO @ Tue, 16 Jun 2020 08:33:43: 5000000 INFO @ Tue, 16 Jun 2020 08:33:48: 1000000 INFO @ Tue, 16 Jun 2020 08:33:49: 11000000 INFO @ Tue, 16 Jun 2020 08:33:50: 6000000 INFO @ Tue, 16 Jun 2020 08:33:55: 2000000 INFO @ Tue, 16 Jun 2020 08:33:55: 12000000 INFO @ Tue, 16 Jun 2020 08:33:56: 7000000 INFO @ Tue, 16 Jun 2020 08:34:01: 3000000 INFO @ Tue, 16 Jun 2020 08:34:01: 13000000 INFO @ Tue, 16 Jun 2020 08:34:03: 8000000 INFO @ Tue, 16 Jun 2020 08:34:08: 14000000 INFO @ Tue, 16 Jun 2020 08:34:08: 4000000 INFO @ Tue, 16 Jun 2020 08:34:09: 9000000 INFO @ Tue, 16 Jun 2020 08:34:11: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:34:11: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:34:11: #1 total tags in treatment: 14388891 INFO @ Tue, 16 Jun 2020 08:34:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:11: #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 08:34:11: #1 tags after filtering in treatment: 14388891 INFO @ Tue, 16 Jun 2020 08:34:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:12: #2 number of paired peaks: 485 WARNING @ Tue, 16 Jun 2020 08:34:12: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:12: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:34:12: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 16 Jun 2020 08:34:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.05_model.r INFO @ Tue, 16 Jun 2020 08:34:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:15: 5000000 INFO @ Tue, 16 Jun 2020 08:34:16: 10000000 INFO @ Tue, 16 Jun 2020 08:34:21: 6000000 INFO @ Tue, 16 Jun 2020 08:34:22: 11000000 INFO @ Tue, 16 Jun 2020 08:34:27: 7000000 INFO @ Tue, 16 Jun 2020 08:34:28: 12000000 INFO @ Tue, 16 Jun 2020 08:34:34: 8000000 INFO @ Tue, 16 Jun 2020 08:34:34: 13000000 INFO @ Tue, 16 Jun 2020 08:34:40: 9000000 INFO @ Tue, 16 Jun 2020 08:34:41: 14000000 INFO @ Tue, 16 Jun 2020 08:34:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:43: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:34:43: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:34:43: #1 total tags in treatment: 14388891 INFO @ Tue, 16 Jun 2020 08:34:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:43: #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 08:34:44: #1 tags after filtering in treatment: 14388891 INFO @ Tue, 16 Jun 2020 08:34:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:45: #2 number of paired peaks: 485 WARNING @ Tue, 16 Jun 2020 08:34:45: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:45: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:34:45: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 16 Jun 2020 08:34:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.10_model.r INFO @ Tue, 16 Jun 2020 08:34:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:46: 10000000 INFO @ Tue, 16 Jun 2020 08:34:53: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.05_summits.bed INFO @ Tue, 16 Jun 2020 08:34:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2519 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:59: 12000000 INFO @ Tue, 16 Jun 2020 08:35:05: 13000000 INFO @ Tue, 16 Jun 2020 08:35:11: 14000000 INFO @ Tue, 16 Jun 2020 08:35:13: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:35:13: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:35:13: #1 total tags in treatment: 14388891 INFO @ Tue, 16 Jun 2020 08:35:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:13: #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 08:35:13: #1 tags after filtering in treatment: 14388891 INFO @ Tue, 16 Jun 2020 08:35:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:14: #2 number of paired peaks: 485 WARNING @ Tue, 16 Jun 2020 08:35:14: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:14: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 08:35:14: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 16 Jun 2020 08:35:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.20_model.r INFO @ Tue, 16 Jun 2020 08:35:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:35:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.10_summits.bed INFO @ Tue, 16 Jun 2020 08:35:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1810 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:35:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576626/SRX2576626.20_summits.bed INFO @ Tue, 16 Jun 2020 08:35:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1242 records, 4 fields): 3 millis CompletedMACS2peakCalling