Job ID = 6367822 SRX = SRX4085390 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:33:05 prefetch.2.10.7: 1) Downloading 'SRR7167419'... 2020-06-15T23:33:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:37:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:37:40 prefetch.2.10.7: 1) 'SRR7167419' was downloaded successfully Read 15430972 spots for SRR7167419/SRR7167419.sra Written 15430972 spots for SRR7167419/SRR7167419.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: 00:08:35 15430972 reads; of these: 15430972 (100.00%) were paired; of these: 8920038 (57.81%) aligned concordantly 0 times 5617983 (36.41%) aligned concordantly exactly 1 time 892951 (5.79%) aligned concordantly >1 times ---- 8920038 pairs aligned concordantly 0 times; of these: 442548 (4.96%) aligned discordantly 1 time ---- 8477490 pairs aligned 0 times concordantly or discordantly; of these: 16954980 mates make up the pairs; of these: 12136519 (71.58%) aligned 0 times 4180900 (24.66%) aligned exactly 1 time 637561 (3.76%) aligned >1 times 60.67% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:35 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] 673829 / 6721314 = 0.1003 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 08:52:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.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 08:52:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:56: 1000000 INFO @ Tue, 16 Jun 2020 08:53:01: 2000000 INFO @ Tue, 16 Jun 2020 08:53:06: 3000000 INFO @ Tue, 16 Jun 2020 08:53:11: 4000000 INFO @ Tue, 16 Jun 2020 08:53:16: 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 08:53:21: 6000000 INFO @ Tue, 16 Jun 2020 08:53:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.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 08:53:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:27: 7000000 INFO @ Tue, 16 Jun 2020 08:53:27: 1000000 INFO @ Tue, 16 Jun 2020 08:53:33: 8000000 INFO @ Tue, 16 Jun 2020 08:53:33: 2000000 INFO @ Tue, 16 Jun 2020 08:53:38: 9000000 INFO @ Tue, 16 Jun 2020 08:53:39: 3000000 INFO @ Tue, 16 Jun 2020 08:53:44: 10000000 INFO @ Tue, 16 Jun 2020 08:53:44: 4000000 INFO @ Tue, 16 Jun 2020 08:53:49: 11000000 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 08:53:50: 5000000 INFO @ Tue, 16 Jun 2020 08:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.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 08:53:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:55: 12000000 INFO @ Tue, 16 Jun 2020 08:53:56: 6000000 INFO @ Tue, 16 Jun 2020 08:53:57: 1000000 INFO @ Tue, 16 Jun 2020 08:54:00: 13000000 INFO @ Tue, 16 Jun 2020 08:54:01: 7000000 INFO @ Tue, 16 Jun 2020 08:54:03: 2000000 INFO @ Tue, 16 Jun 2020 08:54:06: 14000000 INFO @ Tue, 16 Jun 2020 08:54:07: 8000000 INFO @ Tue, 16 Jun 2020 08:54:09: 3000000 INFO @ Tue, 16 Jun 2020 08:54:12: 15000000 INFO @ Tue, 16 Jun 2020 08:54:13: 9000000 INFO @ Tue, 16 Jun 2020 08:54:14: 4000000 INFO @ Tue, 16 Jun 2020 08:54:17: 16000000 INFO @ Tue, 16 Jun 2020 08:54:19: 10000000 INFO @ Tue, 16 Jun 2020 08:54:20: 5000000 INFO @ Tue, 16 Jun 2020 08:54:23: 17000000 INFO @ Tue, 16 Jun 2020 08:54:24: 11000000 INFO @ Tue, 16 Jun 2020 08:54:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:54:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:54:25: #1 total tags in treatment: 5858077 INFO @ Tue, 16 Jun 2020 08:54:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:54:25: #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 08:54:25: #1 tags after filtering in treatment: 5471314 INFO @ Tue, 16 Jun 2020 08:54:25: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 08:54:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:54:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:54:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:54:26: #2 number of paired peaks: 274 WARNING @ Tue, 16 Jun 2020 08:54:26: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 16 Jun 2020 08:54:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:54:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:54:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:54:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:54:26: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 08:54:26: #2 alternative fragment length(s) may be 71,95,123,142,214 bps INFO @ Tue, 16 Jun 2020 08:54:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.05_model.r INFO @ Tue, 16 Jun 2020 08:54:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:54:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:54:26: 6000000 INFO @ Tue, 16 Jun 2020 08:54:30: 12000000 INFO @ Tue, 16 Jun 2020 08:54:32: 7000000 INFO @ Tue, 16 Jun 2020 08:54:36: 13000000 INFO @ Tue, 16 Jun 2020 08:54:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:54:37: 8000000 INFO @ Tue, 16 Jun 2020 08:54:42: 14000000 INFO @ Tue, 16 Jun 2020 08:54:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:54:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:54:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.05_summits.bed INFO @ Tue, 16 Jun 2020 08:54:43: Done! INFO @ Tue, 16 Jun 2020 08:54:43: 9000000 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (251 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:54:47: 15000000 INFO @ Tue, 16 Jun 2020 08:54:49: 10000000 INFO @ Tue, 16 Jun 2020 08:54:53: 16000000 INFO @ Tue, 16 Jun 2020 08:54:55: 11000000 INFO @ Tue, 16 Jun 2020 08:54:59: 17000000 INFO @ Tue, 16 Jun 2020 08:55:01: 12000000 INFO @ Tue, 16 Jun 2020 08:55:01: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:55:01: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:55:01: #1 total tags in treatment: 5858077 INFO @ Tue, 16 Jun 2020 08:55:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:01: #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 08:55:01: #1 tags after filtering in treatment: 5471314 INFO @ Tue, 16 Jun 2020 08:55:01: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 08:55:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:02: #2 number of paired peaks: 274 WARNING @ Tue, 16 Jun 2020 08:55:02: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:02: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 08:55:02: #2 alternative fragment length(s) may be 71,95,123,142,214 bps INFO @ Tue, 16 Jun 2020 08:55:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.10_model.r INFO @ Tue, 16 Jun 2020 08:55:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:06: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:55:11: 14000000 INFO @ Tue, 16 Jun 2020 08:55:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:55:17: 15000000 INFO @ Tue, 16 Jun 2020 08:55:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:55:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:55:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.10_summits.bed INFO @ Tue, 16 Jun 2020 08:55:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:55:22: 16000000 INFO @ Tue, 16 Jun 2020 08:55:27: 17000000 INFO @ Tue, 16 Jun 2020 08:55:29: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:55:29: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:55:29: #1 total tags in treatment: 5858077 INFO @ Tue, 16 Jun 2020 08:55:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:29: #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 08:55:29: #1 tags after filtering in treatment: 5471314 INFO @ Tue, 16 Jun 2020 08:55:29: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 08:55:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:30: #2 number of paired peaks: 274 WARNING @ Tue, 16 Jun 2020 08:55:30: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:30: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 08:55:30: #2 alternative fragment length(s) may be 71,95,123,142,214 bps INFO @ Tue, 16 Jun 2020 08:55:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.20_model.r INFO @ Tue, 16 Jun 2020 08:55:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:55:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:55:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:55:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085390/SRX4085390.20_summits.bed INFO @ Tue, 16 Jun 2020 08:55:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (104 records, 4 fields): 1 millis CompletedMACS2peakCalling