Job ID = 6507727 SRX = SRX1353664 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T12:50:32 prefetch.2.10.7: 1) Downloading 'SRR2722818'... 2020-06-26T12:50:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:53:00 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:53:00 prefetch.2.10.7: 1) 'SRR2722818' was downloaded successfully Read 15191543 spots for SRR2722818/SRR2722818.sra Written 15191543 spots for SRR2722818/SRR2722818.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: 00:15:11 15191543 reads; of these: 15191543 (100.00%) were paired; of these: 971324 (6.39%) aligned concordantly 0 times 11699515 (77.01%) aligned concordantly exactly 1 time 2520704 (16.59%) aligned concordantly >1 times ---- 971324 pairs aligned concordantly 0 times; of these: 505777 (52.07%) aligned discordantly 1 time ---- 465547 pairs aligned 0 times concordantly or discordantly; of these: 931094 mates make up the pairs; of these: 490413 (52.67%) aligned 0 times 221167 (23.75%) aligned exactly 1 time 219514 (23.58%) aligned >1 times 98.39% overall alignment rate Time searching: 00:15:11 Overall time: 00:15:11 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 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 637172 / 14692646 = 0.0434 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 22:20:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.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 22:20:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:20:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:20:42: 1000000 INFO @ Fri, 26 Jun 2020 22:20:47: 2000000 INFO @ Fri, 26 Jun 2020 22:20:53: 3000000 INFO @ Fri, 26 Jun 2020 22:20:59: 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 22:21:05: 5000000 INFO @ Fri, 26 Jun 2020 22:21:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.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 22:21:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:21:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:21:11: 6000000 INFO @ Fri, 26 Jun 2020 22:21:12: 1000000 INFO @ Fri, 26 Jun 2020 22:21:18: 7000000 INFO @ Fri, 26 Jun 2020 22:21:20: 2000000 INFO @ Fri, 26 Jun 2020 22:21:25: 8000000 INFO @ Fri, 26 Jun 2020 22:21:26: 3000000 INFO @ Fri, 26 Jun 2020 22:21:31: 9000000 INFO @ Fri, 26 Jun 2020 22:21:33: 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 22:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.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 22:21:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:21:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:21:38: 10000000 INFO @ Fri, 26 Jun 2020 22:21:39: 5000000 INFO @ Fri, 26 Jun 2020 22:21:42: 1000000 INFO @ Fri, 26 Jun 2020 22:21:44: 11000000 INFO @ Fri, 26 Jun 2020 22:21:46: 6000000 INFO @ Fri, 26 Jun 2020 22:21:49: 2000000 INFO @ Fri, 26 Jun 2020 22:21:51: 12000000 INFO @ Fri, 26 Jun 2020 22:21:53: 7000000 INFO @ Fri, 26 Jun 2020 22:21:56: 3000000 INFO @ Fri, 26 Jun 2020 22:21:57: 13000000 INFO @ Fri, 26 Jun 2020 22:21:59: 8000000 INFO @ Fri, 26 Jun 2020 22:22:02: 4000000 INFO @ Fri, 26 Jun 2020 22:22:04: 14000000 INFO @ Fri, 26 Jun 2020 22:22:06: 9000000 INFO @ Fri, 26 Jun 2020 22:22:09: 5000000 INFO @ Fri, 26 Jun 2020 22:22:10: 15000000 INFO @ Fri, 26 Jun 2020 22:22:12: 10000000 INFO @ Fri, 26 Jun 2020 22:22:15: 6000000 INFO @ Fri, 26 Jun 2020 22:22:17: 16000000 INFO @ Fri, 26 Jun 2020 22:22:19: 11000000 INFO @ Fri, 26 Jun 2020 22:22:22: 7000000 INFO @ Fri, 26 Jun 2020 22:22:23: 17000000 INFO @ Fri, 26 Jun 2020 22:22:25: 12000000 INFO @ Fri, 26 Jun 2020 22:22:28: 8000000 INFO @ Fri, 26 Jun 2020 22:22:29: 18000000 INFO @ Fri, 26 Jun 2020 22:22:32: 13000000 INFO @ Fri, 26 Jun 2020 22:22:34: 9000000 INFO @ Fri, 26 Jun 2020 22:22:36: 19000000 INFO @ Fri, 26 Jun 2020 22:22:38: 14000000 INFO @ Fri, 26 Jun 2020 22:22:41: 10000000 INFO @ Fri, 26 Jun 2020 22:22:42: 20000000 INFO @ Fri, 26 Jun 2020 22:22:45: 15000000 INFO @ Fri, 26 Jun 2020 22:22:47: 11000000 INFO @ Fri, 26 Jun 2020 22:22:48: 21000000 INFO @ Fri, 26 Jun 2020 22:22:51: 16000000 INFO @ Fri, 26 Jun 2020 22:22:54: 12000000 INFO @ Fri, 26 Jun 2020 22:22:54: 22000000 INFO @ Fri, 26 Jun 2020 22:22:57: 17000000 INFO @ Fri, 26 Jun 2020 22:23:00: 13000000 INFO @ Fri, 26 Jun 2020 22:23:01: 23000000 INFO @ Fri, 26 Jun 2020 22:23:04: 18000000 INFO @ Fri, 26 Jun 2020 22:23:06: 14000000 INFO @ Fri, 26 Jun 2020 22:23:07: 24000000 INFO @ Fri, 26 Jun 2020 22:23:10: 19000000 INFO @ Fri, 26 Jun 2020 22:23:13: 15000000 INFO @ Fri, 26 Jun 2020 22:23:13: 25000000 INFO @ Fri, 26 Jun 2020 22:23:16: 20000000 INFO @ Fri, 26 Jun 2020 22:23:19: 16000000 INFO @ Fri, 26 Jun 2020 22:23:20: 26000000 INFO @ Fri, 26 Jun 2020 22:23:22: 21000000 INFO @ Fri, 26 Jun 2020 22:23:25: 17000000 INFO @ Fri, 26 Jun 2020 22:23:26: 27000000 INFO @ Fri, 26 Jun 2020 22:23:29: 22000000 INFO @ Fri, 26 Jun 2020 22:23:32: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:23:32: 28000000 INFO @ Fri, 26 Jun 2020 22:23:35: 23000000 INFO @ Fri, 26 Jun 2020 22:23:36: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:23:36: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:23:36: #1 total tags in treatment: 13590718 INFO @ Fri, 26 Jun 2020 22:23:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:23:36: #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 22:23:36: #1 tags after filtering in treatment: 12416754 INFO @ Fri, 26 Jun 2020 22:23:36: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:23:36: #1 finished! INFO @ Fri, 26 Jun 2020 22:23:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:23:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:23:37: #2 number of paired peaks: 409 WARNING @ Fri, 26 Jun 2020 22:23:37: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Fri, 26 Jun 2020 22:23:37: start model_add_line... INFO @ Fri, 26 Jun 2020 22:23:37: start X-correlation... INFO @ Fri, 26 Jun 2020 22:23:37: end of X-cor INFO @ Fri, 26 Jun 2020 22:23:37: #2 finished! INFO @ Fri, 26 Jun 2020 22:23:37: #2 predicted fragment length is 146 bps INFO @ Fri, 26 Jun 2020 22:23:37: #2 alternative fragment length(s) may be 4,146 bps INFO @ Fri, 26 Jun 2020 22:23:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.05_model.r INFO @ Fri, 26 Jun 2020 22:23:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:23:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:23:38: 19000000 INFO @ Fri, 26 Jun 2020 22:23:42: 24000000 INFO @ Fri, 26 Jun 2020 22:23:44: 20000000 INFO @ Fri, 26 Jun 2020 22:23:48: 25000000 INFO @ Fri, 26 Jun 2020 22:23:51: 21000000 INFO @ Fri, 26 Jun 2020 22:23:54: 26000000 INFO @ Fri, 26 Jun 2020 22:23:57: 22000000 INFO @ Fri, 26 Jun 2020 22:24:01: 27000000 INFO @ Fri, 26 Jun 2020 22:24:03: 23000000 INFO @ Fri, 26 Jun 2020 22:24:04: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:24:07: 28000000 INFO @ Fri, 26 Jun 2020 22:24:10: 24000000 INFO @ Fri, 26 Jun 2020 22:24:11: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:24:11: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:24:11: #1 total tags in treatment: 13590718 INFO @ Fri, 26 Jun 2020 22:24:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:24:11: #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 22:24:11: #1 tags after filtering in treatment: 12416754 INFO @ Fri, 26 Jun 2020 22:24:11: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:24:11: #1 finished! INFO @ Fri, 26 Jun 2020 22:24:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:24:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:24:12: #2 number of paired peaks: 409 WARNING @ Fri, 26 Jun 2020 22:24:12: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Fri, 26 Jun 2020 22:24:12: start model_add_line... INFO @ Fri, 26 Jun 2020 22:24:12: start X-correlation... INFO @ Fri, 26 Jun 2020 22:24:12: end of X-cor INFO @ Fri, 26 Jun 2020 22:24:12: #2 finished! INFO @ Fri, 26 Jun 2020 22:24:12: #2 predicted fragment length is 146 bps INFO @ Fri, 26 Jun 2020 22:24:12: #2 alternative fragment length(s) may be 4,146 bps INFO @ Fri, 26 Jun 2020 22:24:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.10_model.r INFO @ Fri, 26 Jun 2020 22:24:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:24:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:24:16: 25000000 INFO @ Fri, 26 Jun 2020 22:24:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:24:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:24:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.05_summits.bed INFO @ Fri, 26 Jun 2020 22:24:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (400 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:24:22: 26000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:24:27: 27000000 INFO @ Fri, 26 Jun 2020 22:24:33: 28000000 INFO @ Fri, 26 Jun 2020 22:24:37: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:24:37: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:24:37: #1 total tags in treatment: 13590718 INFO @ Fri, 26 Jun 2020 22:24:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:24:37: #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 22:24:37: #1 tags after filtering in treatment: 12416754 INFO @ Fri, 26 Jun 2020 22:24:37: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:24:37: #1 finished! INFO @ Fri, 26 Jun 2020 22:24:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:24:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:24:38: #2 number of paired peaks: 409 WARNING @ Fri, 26 Jun 2020 22:24:38: Fewer paired peaks (409) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 409 pairs to build model! INFO @ Fri, 26 Jun 2020 22:24:38: start model_add_line... INFO @ Fri, 26 Jun 2020 22:24:38: start X-correlation... INFO @ Fri, 26 Jun 2020 22:24:38: end of X-cor INFO @ Fri, 26 Jun 2020 22:24:38: #2 finished! INFO @ Fri, 26 Jun 2020 22:24:38: #2 predicted fragment length is 146 bps INFO @ Fri, 26 Jun 2020 22:24:38: #2 alternative fragment length(s) may be 4,146 bps INFO @ Fri, 26 Jun 2020 22:24:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.20_model.r INFO @ Fri, 26 Jun 2020 22:24:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:24:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:24:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:24:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:24:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:24:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.10_summits.bed INFO @ Fri, 26 Jun 2020 22:24:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (283 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:25:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:25:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:25:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:25:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353664/SRX1353664.20_summits.bed INFO @ Fri, 26 Jun 2020 22:25:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 2 millis CompletedMACS2peakCalling