Job ID = 6507772 SRX = SRX4085363 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:00:26 prefetch.2.10.7: 1) Downloading 'SRR7167392'... 2020-06-26T13:00:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:03:21 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:03:21 prefetch.2.10.7: 1) 'SRR7167392' was downloaded successfully Read 13503380 spots for SRR7167392/SRR7167392.sra Written 13503380 spots for SRR7167392/SRR7167392.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: 00:10:14 13503380 reads; of these: 13503380 (100.00%) were paired; of these: 526641 (3.90%) aligned concordantly 0 times 11496549 (85.14%) aligned concordantly exactly 1 time 1480190 (10.96%) aligned concordantly >1 times ---- 526641 pairs aligned concordantly 0 times; of these: 91927 (17.46%) aligned discordantly 1 time ---- 434714 pairs aligned 0 times concordantly or discordantly; of these: 869428 mates make up the pairs; of these: 468436 (53.88%) aligned 0 times 316000 (36.35%) aligned exactly 1 time 84992 (9.78%) aligned >1 times 98.27% overall alignment rate Time searching: 00:10:14 Overall time: 00:10:14 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 12 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] 1441139 / 13018561 = 0.1107 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 22:21:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.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 22:21:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:21:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:21:58: 1000000 INFO @ Fri, 26 Jun 2020 22:22:05: 2000000 INFO @ Fri, 26 Jun 2020 22:22:12: 3000000 INFO @ Fri, 26 Jun 2020 22:22:19: 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 22:22:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.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 22:22:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:22:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:22:26: 5000000 INFO @ Fri, 26 Jun 2020 22:22:29: 1000000 INFO @ Fri, 26 Jun 2020 22:22:33: 6000000 INFO @ Fri, 26 Jun 2020 22:22:37: 2000000 INFO @ Fri, 26 Jun 2020 22:22:41: 7000000 INFO @ Fri, 26 Jun 2020 22:22:44: 3000000 INFO @ Fri, 26 Jun 2020 22:22:48: 8000000 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 22:22:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.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 22:22:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:22:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:22:52: 4000000 INFO @ Fri, 26 Jun 2020 22:22:56: 9000000 INFO @ Fri, 26 Jun 2020 22:23:00: 5000000 INFO @ Fri, 26 Jun 2020 22:23:00: 1000000 INFO @ Fri, 26 Jun 2020 22:23:04: 10000000 INFO @ Fri, 26 Jun 2020 22:23:07: 6000000 INFO @ Fri, 26 Jun 2020 22:23:08: 2000000 INFO @ Fri, 26 Jun 2020 22:23:12: 11000000 INFO @ Fri, 26 Jun 2020 22:23:15: 7000000 INFO @ Fri, 26 Jun 2020 22:23:17: 3000000 INFO @ Fri, 26 Jun 2020 22:23:20: 12000000 INFO @ Fri, 26 Jun 2020 22:23:23: 8000000 INFO @ Fri, 26 Jun 2020 22:23:25: 4000000 INFO @ Fri, 26 Jun 2020 22:23:27: 13000000 INFO @ Fri, 26 Jun 2020 22:23:31: 9000000 INFO @ Fri, 26 Jun 2020 22:23:34: 5000000 INFO @ Fri, 26 Jun 2020 22:23:35: 14000000 INFO @ Fri, 26 Jun 2020 22:23:39: 10000000 INFO @ Fri, 26 Jun 2020 22:23:42: 6000000 INFO @ Fri, 26 Jun 2020 22:23:43: 15000000 INFO @ Fri, 26 Jun 2020 22:23:46: 11000000 INFO @ Fri, 26 Jun 2020 22:23:50: 7000000 INFO @ Fri, 26 Jun 2020 22:23:52: 16000000 INFO @ Fri, 26 Jun 2020 22:23:54: 12000000 INFO @ Fri, 26 Jun 2020 22:23:58: 8000000 INFO @ Fri, 26 Jun 2020 22:24:00: 17000000 INFO @ Fri, 26 Jun 2020 22:24:02: 13000000 INFO @ Fri, 26 Jun 2020 22:24:06: 9000000 INFO @ Fri, 26 Jun 2020 22:24:08: 18000000 INFO @ Fri, 26 Jun 2020 22:24:09: 14000000 INFO @ Fri, 26 Jun 2020 22:24:14: 10000000 INFO @ Fri, 26 Jun 2020 22:24:16: 19000000 INFO @ Fri, 26 Jun 2020 22:24:17: 15000000 INFO @ Fri, 26 Jun 2020 22:24:22: 11000000 INFO @ Fri, 26 Jun 2020 22:24:25: 20000000 INFO @ Fri, 26 Jun 2020 22:24:25: 16000000 INFO @ Fri, 26 Jun 2020 22:24:30: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:24:33: 17000000 INFO @ Fri, 26 Jun 2020 22:24:33: 21000000 INFO @ Fri, 26 Jun 2020 22:24:38: 13000000 INFO @ Fri, 26 Jun 2020 22:24:41: 18000000 INFO @ Fri, 26 Jun 2020 22:24:41: 22000000 INFO @ Fri, 26 Jun 2020 22:24:46: 14000000 INFO @ Fri, 26 Jun 2020 22:24:48: 19000000 INFO @ Fri, 26 Jun 2020 22:24:49: 23000000 INFO @ Fri, 26 Jun 2020 22:24:54: 15000000 INFO @ Fri, 26 Jun 2020 22:24:55: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:24:55: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:24:55: #1 total tags in treatment: 11538578 INFO @ Fri, 26 Jun 2020 22:24:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:24:55: #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 22:24:55: #1 tags after filtering in treatment: 10414578 INFO @ Fri, 26 Jun 2020 22:24:55: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 22:24:55: #1 finished! INFO @ Fri, 26 Jun 2020 22:24:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:24:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:24:55: #2 number of paired peaks: 167 WARNING @ Fri, 26 Jun 2020 22:24:55: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 26 Jun 2020 22:24:55: start model_add_line... INFO @ Fri, 26 Jun 2020 22:24:56: start X-correlation... INFO @ Fri, 26 Jun 2020 22:24:56: end of X-cor INFO @ Fri, 26 Jun 2020 22:24:56: #2 finished! INFO @ Fri, 26 Jun 2020 22:24:56: #2 predicted fragment length is 145 bps INFO @ Fri, 26 Jun 2020 22:24:56: #2 alternative fragment length(s) may be 4,125,145,174 bps INFO @ Fri, 26 Jun 2020 22:24:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.05_model.r INFO @ Fri, 26 Jun 2020 22:24:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:24:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:24:56: 20000000 INFO @ Fri, 26 Jun 2020 22:25:01: 16000000 INFO @ Fri, 26 Jun 2020 22:25:04: 21000000 INFO @ Fri, 26 Jun 2020 22:25:09: 17000000 INFO @ Fri, 26 Jun 2020 22:25:11: 22000000 INFO @ Fri, 26 Jun 2020 22:25:16: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:25:17: 18000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:25:19: 23000000 INFO @ Fri, 26 Jun 2020 22:25:24: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:25:24: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:25:24: #1 total tags in treatment: 11538578 INFO @ Fri, 26 Jun 2020 22:25:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:25:24: #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 22:25:24: #1 tags after filtering in treatment: 10414578 INFO @ Fri, 26 Jun 2020 22:25:24: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 22:25:24: #1 finished! INFO @ Fri, 26 Jun 2020 22:25:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:25:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:25:25: 19000000 INFO @ Fri, 26 Jun 2020 22:25:25: #2 number of paired peaks: 167 WARNING @ Fri, 26 Jun 2020 22:25:25: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 26 Jun 2020 22:25:25: start model_add_line... INFO @ Fri, 26 Jun 2020 22:25:25: start X-correlation... INFO @ Fri, 26 Jun 2020 22:25:25: end of X-cor INFO @ Fri, 26 Jun 2020 22:25:25: #2 finished! INFO @ Fri, 26 Jun 2020 22:25:25: #2 predicted fragment length is 145 bps INFO @ Fri, 26 Jun 2020 22:25:25: #2 alternative fragment length(s) may be 4,125,145,174 bps INFO @ Fri, 26 Jun 2020 22:25:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.10_model.r INFO @ Fri, 26 Jun 2020 22:25:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:25:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:25:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:25:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:25:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.05_summits.bed INFO @ Fri, 26 Jun 2020 22:25:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (236 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:25:32: 20000000 INFO @ Fri, 26 Jun 2020 22:25:39: 21000000 INFO @ Fri, 26 Jun 2020 22:25:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:25:46: 22000000 INFO @ Fri, 26 Jun 2020 22:25:53: 23000000 INFO @ Fri, 26 Jun 2020 22:25:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:25:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:25:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.10_summits.bed INFO @ Fri, 26 Jun 2020 22:25:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (169 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:25:57: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:25:57: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:25:57: #1 total tags in treatment: 11538578 INFO @ Fri, 26 Jun 2020 22:25:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:25:57: #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 22:25:58: #1 tags after filtering in treatment: 10414578 INFO @ Fri, 26 Jun 2020 22:25:58: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 22:25:58: #1 finished! INFO @ Fri, 26 Jun 2020 22:25:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:25:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:25:58: #2 number of paired peaks: 167 WARNING @ Fri, 26 Jun 2020 22:25:58: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 26 Jun 2020 22:25:58: start model_add_line... INFO @ Fri, 26 Jun 2020 22:25:58: start X-correlation... INFO @ Fri, 26 Jun 2020 22:25:58: end of X-cor INFO @ Fri, 26 Jun 2020 22:25:58: #2 finished! INFO @ Fri, 26 Jun 2020 22:25:58: #2 predicted fragment length is 145 bps INFO @ Fri, 26 Jun 2020 22:25:58: #2 alternative fragment length(s) may be 4,125,145,174 bps INFO @ Fri, 26 Jun 2020 22:25:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.20_model.r INFO @ Fri, 26 Jun 2020 22:25:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:25:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:26:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085363/SRX4085363.20_summits.bed INFO @ Fri, 26 Jun 2020 22:26:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (104 records, 4 fields): 1 millis CompletedMACS2peakCalling