Job ID = 6507869 SRX = SRX494950 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T12:47:03 prefetch.2.10.7: 1) Downloading 'SRR1198482'... 2020-06-26T12:47:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:49:18 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:49:18 prefetch.2.10.7: 1) 'SRR1198482' was downloaded successfully Read 25949020 spots for SRR1198482/SRR1198482.sra Written 25949020 spots for SRR1198482/SRR1198482.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: 00:03:31 25949020 reads; of these: 25949020 (100.00%) were unpaired; of these: 4649944 (17.92%) aligned 0 times 17939397 (69.13%) aligned exactly 1 time 3359679 (12.95%) aligned >1 times 82.08% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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] 7818210 / 21299076 = 0.3671 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 @ Fri, 26 Jun 2020 21:58:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.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 @ Fri, 26 Jun 2020 21:58:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:58:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:58:27: 1000000 INFO @ Fri, 26 Jun 2020 21:58:33: 2000000 INFO @ Fri, 26 Jun 2020 21:58:39: 3000000 INFO @ Fri, 26 Jun 2020 21:58:45: 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 @ Fri, 26 Jun 2020 21:58:51: 5000000 INFO @ Fri, 26 Jun 2020 21:58:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.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 @ Fri, 26 Jun 2020 21:58:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:58:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:58:57: 6000000 INFO @ Fri, 26 Jun 2020 21:58:58: 1000000 INFO @ Fri, 26 Jun 2020 21:59:03: 7000000 INFO @ Fri, 26 Jun 2020 21:59:04: 2000000 INFO @ Fri, 26 Jun 2020 21:59:09: 8000000 INFO @ Fri, 26 Jun 2020 21:59:10: 3000000 INFO @ Fri, 26 Jun 2020 21:59:15: 9000000 INFO @ Fri, 26 Jun 2020 21:59:17: 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 @ Fri, 26 Jun 2020 21:59:21: 10000000 INFO @ Fri, 26 Jun 2020 21:59:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.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 @ Fri, 26 Jun 2020 21:59:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:59:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:59:23: 5000000 INFO @ Fri, 26 Jun 2020 21:59:28: 11000000 INFO @ Fri, 26 Jun 2020 21:59:28: 1000000 INFO @ Fri, 26 Jun 2020 21:59:29: 6000000 INFO @ Fri, 26 Jun 2020 21:59:34: 12000000 INFO @ Fri, 26 Jun 2020 21:59:34: 2000000 INFO @ Fri, 26 Jun 2020 21:59:36: 7000000 INFO @ Fri, 26 Jun 2020 21:59:40: 13000000 INFO @ Fri, 26 Jun 2020 21:59:41: 3000000 INFO @ Fri, 26 Jun 2020 21:59:42: 8000000 INFO @ Fri, 26 Jun 2020 21:59:43: #1 tag size is determined as 35 bps INFO @ Fri, 26 Jun 2020 21:59:43: #1 tag size = 35 INFO @ Fri, 26 Jun 2020 21:59:43: #1 total tags in treatment: 13480866 INFO @ Fri, 26 Jun 2020 21:59:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 21:59:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 21:59:43: #1 tags after filtering in treatment: 13480866 INFO @ Fri, 26 Jun 2020 21:59:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 21:59:43: #1 finished! INFO @ Fri, 26 Jun 2020 21:59:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 21:59:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 21:59:44: #2 number of paired peaks: 222 WARNING @ Fri, 26 Jun 2020 21:59:44: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Fri, 26 Jun 2020 21:59:44: start model_add_line... INFO @ Fri, 26 Jun 2020 21:59:44: start X-correlation... INFO @ Fri, 26 Jun 2020 21:59:44: end of X-cor INFO @ Fri, 26 Jun 2020 21:59:44: #2 finished! INFO @ Fri, 26 Jun 2020 21:59:44: #2 predicted fragment length is 135 bps INFO @ Fri, 26 Jun 2020 21:59:44: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 26 Jun 2020 21:59:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.05_model.r INFO @ Fri, 26 Jun 2020 21:59:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 21:59:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 21:59:47: 4000000 INFO @ Fri, 26 Jun 2020 21:59:48: 9000000 INFO @ Fri, 26 Jun 2020 21:59:53: 5000000 INFO @ Fri, 26 Jun 2020 21:59:55: 10000000 INFO @ Fri, 26 Jun 2020 22:00:00: 6000000 INFO @ Fri, 26 Jun 2020 22:00:01: 11000000 INFO @ Fri, 26 Jun 2020 22:00:06: 7000000 INFO @ Fri, 26 Jun 2020 22:00:07: 12000000 INFO @ Fri, 26 Jun 2020 22:00:12: 8000000 INFO @ Fri, 26 Jun 2020 22:00:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:00:14: 13000000 INFO @ Fri, 26 Jun 2020 22:00:17: #1 tag size is determined as 35 bps INFO @ Fri, 26 Jun 2020 22:00:17: #1 tag size = 35 INFO @ Fri, 26 Jun 2020 22:00:17: #1 total tags in treatment: 13480866 INFO @ Fri, 26 Jun 2020 22:00:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:00:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:00:17: #1 tags after filtering in treatment: 13480866 INFO @ Fri, 26 Jun 2020 22:00:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:00:17: #1 finished! INFO @ Fri, 26 Jun 2020 22:00:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:00:18: #2 number of paired peaks: 222 WARNING @ Fri, 26 Jun 2020 22:00:18: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Fri, 26 Jun 2020 22:00:18: start model_add_line... INFO @ Fri, 26 Jun 2020 22:00:18: start X-correlation... INFO @ Fri, 26 Jun 2020 22:00:18: end of X-cor INFO @ Fri, 26 Jun 2020 22:00:18: #2 finished! INFO @ Fri, 26 Jun 2020 22:00:18: #2 predicted fragment length is 135 bps INFO @ Fri, 26 Jun 2020 22:00:18: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 26 Jun 2020 22:00:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.10_model.r INFO @ Fri, 26 Jun 2020 22:00:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:00:18: 9000000 INFO @ Fri, 26 Jun 2020 22:00:25: 10000000 INFO @ Fri, 26 Jun 2020 22:00:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:00:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:00:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.05_summits.bed INFO @ Fri, 26 Jun 2020 22:00:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7464 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:00:30: 11000000 INFO @ Fri, 26 Jun 2020 22:00:37: 12000000 INFO @ Fri, 26 Jun 2020 22:00:43: 13000000 INFO @ Fri, 26 Jun 2020 22:00:45: #1 tag size is determined as 35 bps INFO @ Fri, 26 Jun 2020 22:00:45: #1 tag size = 35 INFO @ Fri, 26 Jun 2020 22:00:45: #1 total tags in treatment: 13480866 INFO @ Fri, 26 Jun 2020 22:00:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:00:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:00:46: #1 tags after filtering in treatment: 13480866 INFO @ Fri, 26 Jun 2020 22:00:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:00:46: #1 finished! INFO @ Fri, 26 Jun 2020 22:00:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:00:47: #2 number of paired peaks: 222 WARNING @ Fri, 26 Jun 2020 22:00:47: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Fri, 26 Jun 2020 22:00:47: start model_add_line... INFO @ Fri, 26 Jun 2020 22:00:47: start X-correlation... INFO @ Fri, 26 Jun 2020 22:00:47: end of X-cor INFO @ Fri, 26 Jun 2020 22:00:47: #2 finished! INFO @ Fri, 26 Jun 2020 22:00:47: #2 predicted fragment length is 135 bps INFO @ Fri, 26 Jun 2020 22:00:47: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 26 Jun 2020 22:00:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.20_model.r INFO @ Fri, 26 Jun 2020 22:00:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:00:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:00:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.10_summits.bed INFO @ Fri, 26 Jun 2020 22:01:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3482 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:01:16: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:01:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:01:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:01:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494950/SRX494950.20_summits.bed INFO @ Fri, 26 Jun 2020 22:01:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1299 records, 4 fields): 3 millis CompletedMACS2peakCalling