Job ID = 6367829 SRX = SRX4085397 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:35:59 prefetch.2.10.7: 1) Downloading 'SRR7167426'... 2020-06-15T23:35:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:38 prefetch.2.10.7: 1) 'SRR7167426' was downloaded successfully Read 37938920 spots for SRR7167426/SRR7167426.sra Written 37938920 spots for SRR7167426/SRR7167426.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: 00:30:22 37938920 reads; of these: 37938920 (100.00%) were paired; of these: 3083448 (8.13%) aligned concordantly 0 times 30970038 (81.63%) aligned concordantly exactly 1 time 3885434 (10.24%) aligned concordantly >1 times ---- 3083448 pairs aligned concordantly 0 times; of these: 1182245 (38.34%) aligned discordantly 1 time ---- 1901203 pairs aligned 0 times concordantly or discordantly; of these: 3802406 mates make up the pairs; of these: 2325985 (61.17%) aligned 0 times 950675 (25.00%) aligned exactly 1 time 525746 (13.83%) aligned >1 times 96.93% overall alignment rate Time searching: 00:30:22 Overall time: 00:30:22 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 32 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] 25772568 / 35098417 = 0.7343 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 09:39:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.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 09:39:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:53: 1000000 INFO @ Tue, 16 Jun 2020 09:39:58: 2000000 INFO @ Tue, 16 Jun 2020 09:40:04: 3000000 INFO @ Tue, 16 Jun 2020 09:40:09: 4000000 INFO @ Tue, 16 Jun 2020 09:40:15: 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 09:40:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.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 09:40:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:20: 6000000 INFO @ Tue, 16 Jun 2020 09:40:23: 1000000 INFO @ Tue, 16 Jun 2020 09:40:26: 7000000 INFO @ Tue, 16 Jun 2020 09:40:29: 2000000 INFO @ Tue, 16 Jun 2020 09:40:32: 8000000 INFO @ Tue, 16 Jun 2020 09:40:34: 3000000 INFO @ Tue, 16 Jun 2020 09:40:38: 9000000 INFO @ Tue, 16 Jun 2020 09:40:40: 4000000 INFO @ Tue, 16 Jun 2020 09:40:44: 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 09:40:46: 5000000 INFO @ Tue, 16 Jun 2020 09:40:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.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 09:40:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:50: 11000000 INFO @ Tue, 16 Jun 2020 09:40:51: 6000000 INFO @ Tue, 16 Jun 2020 09:40:53: 1000000 INFO @ Tue, 16 Jun 2020 09:40:55: 12000000 INFO @ Tue, 16 Jun 2020 09:40:57: 7000000 INFO @ Tue, 16 Jun 2020 09:40:59: 2000000 INFO @ Tue, 16 Jun 2020 09:41:01: 13000000 INFO @ Tue, 16 Jun 2020 09:41:03: 8000000 INFO @ Tue, 16 Jun 2020 09:41:05: 3000000 INFO @ Tue, 16 Jun 2020 09:41:07: 14000000 INFO @ Tue, 16 Jun 2020 09:41:09: 9000000 INFO @ Tue, 16 Jun 2020 09:41:11: 4000000 INFO @ Tue, 16 Jun 2020 09:41:13: 15000000 INFO @ Tue, 16 Jun 2020 09:41:15: 10000000 INFO @ Tue, 16 Jun 2020 09:41:17: 5000000 INFO @ Tue, 16 Jun 2020 09:41:19: 16000000 INFO @ Tue, 16 Jun 2020 09:41:21: 11000000 INFO @ Tue, 16 Jun 2020 09:41:23: 6000000 INFO @ Tue, 16 Jun 2020 09:41:25: 17000000 INFO @ Tue, 16 Jun 2020 09:41:27: 12000000 INFO @ Tue, 16 Jun 2020 09:41:29: 7000000 INFO @ Tue, 16 Jun 2020 09:41:31: 18000000 INFO @ Tue, 16 Jun 2020 09:41:33: 13000000 INFO @ Tue, 16 Jun 2020 09:41:35: 8000000 INFO @ Tue, 16 Jun 2020 09:41:37: 19000000 INFO @ Tue, 16 Jun 2020 09:41:39: 14000000 INFO @ Tue, 16 Jun 2020 09:41:41: 9000000 INFO @ Tue, 16 Jun 2020 09:41:43: 20000000 INFO @ Tue, 16 Jun 2020 09:41:45: 15000000 INFO @ Tue, 16 Jun 2020 09:41:47: 10000000 INFO @ Tue, 16 Jun 2020 09:41:48: 21000000 INFO @ Tue, 16 Jun 2020 09:41:51: 16000000 INFO @ Tue, 16 Jun 2020 09:41:53: 11000000 INFO @ Tue, 16 Jun 2020 09:41:54: 22000000 INFO @ Tue, 16 Jun 2020 09:41:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:41:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:41:54: #1 total tags in treatment: 9261568 INFO @ Tue, 16 Jun 2020 09:41:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:54: #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 09:41:54: #1 tags after filtering in treatment: 7552867 INFO @ Tue, 16 Jun 2020 09:41:54: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 16 Jun 2020 09:41:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:55: #2 number of paired peaks: 727 WARNING @ Tue, 16 Jun 2020 09:41:55: Fewer paired peaks (727) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 727 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:55: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 09:41:55: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 16 Jun 2020 09:41:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.05_model.r INFO @ Tue, 16 Jun 2020 09:41:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:57: 17000000 INFO @ Tue, 16 Jun 2020 09:41:58: 12000000 INFO @ Tue, 16 Jun 2020 09:42:02: 18000000 INFO @ Tue, 16 Jun 2020 09:42:04: 13000000 INFO @ Tue, 16 Jun 2020 09:42:08: 19000000 INFO @ Tue, 16 Jun 2020 09:42:10: 14000000 INFO @ Tue, 16 Jun 2020 09:42:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:14: 20000000 INFO @ Tue, 16 Jun 2020 09:42:16: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:42:20: 21000000 INFO @ Tue, 16 Jun 2020 09:42:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.05_summits.bed INFO @ Tue, 16 Jun 2020 09:42:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3697 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:22: 16000000 INFO @ Tue, 16 Jun 2020 09:42:25: 22000000 INFO @ Tue, 16 Jun 2020 09:42:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:42:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:42:25: #1 total tags in treatment: 9261568 INFO @ Tue, 16 Jun 2020 09:42:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:25: #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 09:42:25: #1 tags after filtering in treatment: 7552867 INFO @ Tue, 16 Jun 2020 09:42:25: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 16 Jun 2020 09:42:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:26: #2 number of paired peaks: 727 WARNING @ Tue, 16 Jun 2020 09:42:26: Fewer paired peaks (727) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 727 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:26: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 09:42:26: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 16 Jun 2020 09:42:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.10_model.r INFO @ Tue, 16 Jun 2020 09:42:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:28: 17000000 INFO @ Tue, 16 Jun 2020 09:42:33: 18000000 INFO @ Tue, 16 Jun 2020 09:42:39: 19000000 INFO @ Tue, 16 Jun 2020 09:42:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:44: 20000000 INFO @ Tue, 16 Jun 2020 09:42:50: 21000000 INFO @ Tue, 16 Jun 2020 09:42:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.10_summits.bed INFO @ Tue, 16 Jun 2020 09:42:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2234 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:42:55: 22000000 INFO @ Tue, 16 Jun 2020 09:42:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:42:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:42:55: #1 total tags in treatment: 9261568 INFO @ Tue, 16 Jun 2020 09:42:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:55: #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 09:42:55: #1 tags after filtering in treatment: 7552867 INFO @ Tue, 16 Jun 2020 09:42:55: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 16 Jun 2020 09:42:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:56: #2 number of paired peaks: 727 WARNING @ Tue, 16 Jun 2020 09:42:56: Fewer paired peaks (727) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 727 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:56: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 09:42:56: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 16 Jun 2020 09:42:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.20_model.r INFO @ Tue, 16 Jun 2020 09:42:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085397/SRX4085397.20_summits.bed INFO @ Tue, 16 Jun 2020 09:43:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1116 records, 4 fields): 3 millis CompletedMACS2peakCalling