Job ID = 6497453 SRX = SRX494950 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:33:05 prefetch.2.10.7: 1) Downloading 'SRR1198482'... 2020-06-25T22:33:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:35:54 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:35:54 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: 00:03:09 25949020 reads; of these: 25949020 (100.00%) were unpaired; of these: 4652580 (17.93%) aligned 0 times 17936920 (69.12%) aligned exactly 1 time 3359520 (12.95%) aligned >1 times 82.07% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 7817145 / 21296440 = 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 07:44:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:44:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:44:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:44:13: 1000000 INFO @ Fri, 26 Jun 2020 07:44:18: 2000000 INFO @ Fri, 26 Jun 2020 07:44:23: 3000000 INFO @ Fri, 26 Jun 2020 07:44:28: 4000000 INFO @ Fri, 26 Jun 2020 07:44:33: 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 @ Fri, 26 Jun 2020 07:44:38: 6000000 INFO @ Fri, 26 Jun 2020 07:44:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:44:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:44:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:44:43: 7000000 INFO @ Fri, 26 Jun 2020 07:44:43: 1000000 INFO @ Fri, 26 Jun 2020 07:44:49: 8000000 INFO @ Fri, 26 Jun 2020 07:44:49: 2000000 INFO @ Fri, 26 Jun 2020 07:44:54: 9000000 INFO @ Fri, 26 Jun 2020 07:44:55: 3000000 INFO @ Fri, 26 Jun 2020 07:45:00: 10000000 INFO @ Fri, 26 Jun 2020 07:45:00: 4000000 INFO @ Fri, 26 Jun 2020 07:45:05: 11000000 INFO @ Fri, 26 Jun 2020 07:45:06: 5000000 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 07:45:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:45:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:45:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:45:11: 12000000 INFO @ Fri, 26 Jun 2020 07:45:11: 6000000 INFO @ Fri, 26 Jun 2020 07:45:13: 1000000 INFO @ Fri, 26 Jun 2020 07:45:16: 13000000 INFO @ Fri, 26 Jun 2020 07:45:17: 7000000 INFO @ Fri, 26 Jun 2020 07:45:19: #1 tag size is determined as 35 bps INFO @ Fri, 26 Jun 2020 07:45:19: #1 tag size = 35 INFO @ Fri, 26 Jun 2020 07:45:19: #1 total tags in treatment: 13479295 INFO @ Fri, 26 Jun 2020 07:45:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:45:19: #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 07:45:19: #1 tags after filtering in treatment: 13479295 INFO @ Fri, 26 Jun 2020 07:45:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:45:19: #1 finished! INFO @ Fri, 26 Jun 2020 07:45:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:45:19: 2000000 INFO @ Fri, 26 Jun 2020 07:45:20: #2 number of paired peaks: 222 WARNING @ Fri, 26 Jun 2020 07:45:20: 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 07:45:20: start model_add_line... INFO @ Fri, 26 Jun 2020 07:45:20: start X-correlation... INFO @ Fri, 26 Jun 2020 07:45:20: end of X-cor INFO @ Fri, 26 Jun 2020 07:45:20: #2 finished! INFO @ Fri, 26 Jun 2020 07:45:20: #2 predicted fragment length is 137 bps INFO @ Fri, 26 Jun 2020 07:45:20: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 26 Jun 2020 07:45:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.05_model.r INFO @ Fri, 26 Jun 2020 07:45:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:45:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:45:22: 8000000 INFO @ Fri, 26 Jun 2020 07:45:25: 3000000 INFO @ Fri, 26 Jun 2020 07:45:28: 9000000 INFO @ Fri, 26 Jun 2020 07:45:30: 4000000 INFO @ Fri, 26 Jun 2020 07:45:33: 10000000 INFO @ Fri, 26 Jun 2020 07:45:36: 5000000 INFO @ Fri, 26 Jun 2020 07:45:39: 11000000 INFO @ Fri, 26 Jun 2020 07:45:41: 6000000 INFO @ Fri, 26 Jun 2020 07:45:44: 12000000 INFO @ Fri, 26 Jun 2020 07:45:47: 7000000 INFO @ Fri, 26 Jun 2020 07:45:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:45:50: 13000000 INFO @ Fri, 26 Jun 2020 07:45:52: 8000000 INFO @ Fri, 26 Jun 2020 07:45:53: #1 tag size is determined as 35 bps INFO @ Fri, 26 Jun 2020 07:45:53: #1 tag size = 35 INFO @ Fri, 26 Jun 2020 07:45:53: #1 total tags in treatment: 13479295 INFO @ Fri, 26 Jun 2020 07:45:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:45:53: #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 07:45:53: #1 tags after filtering in treatment: 13479295 INFO @ Fri, 26 Jun 2020 07:45:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:45:53: #1 finished! INFO @ Fri, 26 Jun 2020 07:45:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:45:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:45:54: #2 number of paired peaks: 222 WARNING @ Fri, 26 Jun 2020 07:45:54: 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 07:45:54: start model_add_line... INFO @ Fri, 26 Jun 2020 07:45:54: start X-correlation... INFO @ Fri, 26 Jun 2020 07:45:54: end of X-cor INFO @ Fri, 26 Jun 2020 07:45:54: #2 finished! INFO @ Fri, 26 Jun 2020 07:45:54: #2 predicted fragment length is 137 bps INFO @ Fri, 26 Jun 2020 07:45:54: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 26 Jun 2020 07:45:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.10_model.r INFO @ Fri, 26 Jun 2020 07:45:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:45:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:45:57: 9000000 INFO @ Fri, 26 Jun 2020 07:46:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:46:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:46:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.05_summits.bed INFO @ Fri, 26 Jun 2020 07:46:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7282 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:46:03: 10000000 INFO @ Fri, 26 Jun 2020 07:46:08: 11000000 INFO @ Fri, 26 Jun 2020 07:46:13: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:46:18: 13000000 INFO @ Fri, 26 Jun 2020 07:46:21: #1 tag size is determined as 35 bps INFO @ Fri, 26 Jun 2020 07:46:21: #1 tag size = 35 INFO @ Fri, 26 Jun 2020 07:46:21: #1 total tags in treatment: 13479295 INFO @ Fri, 26 Jun 2020 07:46:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:46:21: #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 07:46:21: #1 tags after filtering in treatment: 13479295 INFO @ Fri, 26 Jun 2020 07:46:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:46:21: #1 finished! INFO @ Fri, 26 Jun 2020 07:46:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:46:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:46:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:46:22: #2 number of paired peaks: 222 WARNING @ Fri, 26 Jun 2020 07:46:22: 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 07:46:22: start model_add_line... INFO @ Fri, 26 Jun 2020 07:46:22: start X-correlation... INFO @ Fri, 26 Jun 2020 07:46:22: end of X-cor INFO @ Fri, 26 Jun 2020 07:46:22: #2 finished! INFO @ Fri, 26 Jun 2020 07:46:22: #2 predicted fragment length is 137 bps INFO @ Fri, 26 Jun 2020 07:46:22: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 26 Jun 2020 07:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.20_model.r INFO @ Fri, 26 Jun 2020 07:46:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:46:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:46:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:46:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.10_summits.bed INFO @ Fri, 26 Jun 2020 07:46:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3518 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:46:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:47:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:47:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:47:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494950/SRX494950.20_summits.bed INFO @ Fri, 26 Jun 2020 07:47:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1285 records, 4 fields): 3 millis CompletedMACS2peakCalling