Job ID = 6367865 SRX = SRX4085432 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:36:44 prefetch.2.10.7: 1) Downloading 'SRR7167461'... 2020-06-15T23:36:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:03 prefetch.2.10.7: 1) 'SRR7167461' was downloaded successfully Read 8102108 spots for SRR7167461/SRR7167461.sra Written 8102108 spots for SRR7167461/SRR7167461.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: 00:06:41 8102108 reads; of these: 8102108 (100.00%) were paired; of these: 835387 (10.31%) aligned concordantly 0 times 6384684 (78.80%) aligned concordantly exactly 1 time 882037 (10.89%) aligned concordantly >1 times ---- 835387 pairs aligned concordantly 0 times; of these: 413973 (49.55%) aligned discordantly 1 time ---- 421414 pairs aligned 0 times concordantly or discordantly; of these: 842828 mates make up the pairs; of these: 329580 (39.10%) aligned 0 times 318408 (37.78%) aligned exactly 1 time 194840 (23.12%) aligned >1 times 97.97% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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_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] 1544361 / 7361916 = 0.2098 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 08:52:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.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 08:52:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:02: 1000000 INFO @ Tue, 16 Jun 2020 08:53:07: 2000000 INFO @ Tue, 16 Jun 2020 08:53:12: 3000000 INFO @ Tue, 16 Jun 2020 08:53:18: 4000000 INFO @ Tue, 16 Jun 2020 08:53:23: 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 @ Tue, 16 Jun 2020 08:53:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.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 08:53:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:28: 6000000 INFO @ Tue, 16 Jun 2020 08:53:32: 1000000 INFO @ Tue, 16 Jun 2020 08:53:34: 7000000 INFO @ Tue, 16 Jun 2020 08:53:38: 2000000 INFO @ Tue, 16 Jun 2020 08:53:40: 8000000 INFO @ Tue, 16 Jun 2020 08:53:44: 3000000 INFO @ Tue, 16 Jun 2020 08:53:46: 9000000 INFO @ Tue, 16 Jun 2020 08:53:49: 4000000 INFO @ Tue, 16 Jun 2020 08:53:52: 10000000 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 08:53:55: 5000000 INFO @ Tue, 16 Jun 2020 08:53:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.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 08:53:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:58: 11000000 INFO @ Tue, 16 Jun 2020 08:54:01: 6000000 INFO @ Tue, 16 Jun 2020 08:54:03: 1000000 INFO @ Tue, 16 Jun 2020 08:54:04: 12000000 INFO @ Tue, 16 Jun 2020 08:54:07: 7000000 INFO @ Tue, 16 Jun 2020 08:54:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:54:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:54:08: #1 total tags in treatment: 5741464 INFO @ Tue, 16 Jun 2020 08:54:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:54:08: #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 08:54:08: 2000000 INFO @ Tue, 16 Jun 2020 08:54:08: #1 tags after filtering in treatment: 5367252 INFO @ Tue, 16 Jun 2020 08:54:08: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 08:54:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:54:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:54:09: #2 number of paired peaks: 311 WARNING @ Tue, 16 Jun 2020 08:54:09: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 16 Jun 2020 08:54:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:54:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:54:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:54:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:54:09: #2 predicted fragment length is 155 bps INFO @ Tue, 16 Jun 2020 08:54:09: #2 alternative fragment length(s) may be 4,127,155 bps INFO @ Tue, 16 Jun 2020 08:54:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.05_model.r INFO @ Tue, 16 Jun 2020 08:54:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:54:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:54:13: 8000000 INFO @ Tue, 16 Jun 2020 08:54:14: 3000000 INFO @ Tue, 16 Jun 2020 08:54:19: 9000000 INFO @ Tue, 16 Jun 2020 08:54:20: 4000000 INFO @ Tue, 16 Jun 2020 08:54:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:54:25: 10000000 INFO @ Tue, 16 Jun 2020 08:54:26: 5000000 INFO @ Tue, 16 Jun 2020 08:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:54:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:54:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.05_summits.bed INFO @ Tue, 16 Jun 2020 08:54:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:54:30: 11000000 INFO @ Tue, 16 Jun 2020 08:54:31: 6000000 INFO @ Tue, 16 Jun 2020 08:54:36: 12000000 INFO @ Tue, 16 Jun 2020 08:54:37: 7000000 INFO @ Tue, 16 Jun 2020 08:54:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:54:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:54:41: #1 total tags in treatment: 5741464 INFO @ Tue, 16 Jun 2020 08:54:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:54:41: #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 08:54:41: #1 tags after filtering in treatment: 5367252 INFO @ Tue, 16 Jun 2020 08:54:41: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 08:54:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:54:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:54:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:54:41: #2 number of paired peaks: 311 WARNING @ Tue, 16 Jun 2020 08:54:41: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 16 Jun 2020 08:54:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:54:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:54:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:54:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:54:42: #2 predicted fragment length is 155 bps INFO @ Tue, 16 Jun 2020 08:54:42: #2 alternative fragment length(s) may be 4,127,155 bps INFO @ Tue, 16 Jun 2020 08:54:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.10_model.r INFO @ Tue, 16 Jun 2020 08:54:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:54:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:54:43: 8000000 INFO @ Tue, 16 Jun 2020 08:54:48: 9000000 INFO @ Tue, 16 Jun 2020 08:54:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:54:54: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:54:59: 11000000 INFO @ Tue, 16 Jun 2020 08:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.10_summits.bed INFO @ Tue, 16 Jun 2020 08:55:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:55:05: 12000000 INFO @ Tue, 16 Jun 2020 08:55:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:55:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:55:09: #1 total tags in treatment: 5741464 INFO @ Tue, 16 Jun 2020 08:55:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:09: #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 08:55:09: #1 tags after filtering in treatment: 5367252 INFO @ Tue, 16 Jun 2020 08:55:09: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 08:55:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:09: #2 number of paired peaks: 311 WARNING @ Tue, 16 Jun 2020 08:55:09: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:09: #2 predicted fragment length is 155 bps INFO @ Tue, 16 Jun 2020 08:55:09: #2 alternative fragment length(s) may be 4,127,155 bps INFO @ Tue, 16 Jun 2020 08:55:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.20_model.r INFO @ Tue, 16 Jun 2020 08:55:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:55:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:55:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:55:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085432/SRX4085432.20_summits.bed INFO @ Tue, 16 Jun 2020 08:55:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (103 records, 4 fields): 1 millis CompletedMACS2peakCalling