Job ID = 6367827 SRX = SRX4085395 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:56:27 prefetch.2.10.7: 1) Downloading 'SRR7167424'... 2020-06-15T23:56:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:04:45 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:04:45 prefetch.2.10.7: 1) 'SRR7167424' was downloaded successfully Read 44130800 spots for SRR7167424/SRR7167424.sra Written 44130800 spots for SRR7167424/SRR7167424.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: 00:33:54 44130800 reads; of these: 44130800 (100.00%) were paired; of these: 3016229 (6.83%) aligned concordantly 0 times 36843674 (83.49%) aligned concordantly exactly 1 time 4270897 (9.68%) aligned concordantly >1 times ---- 3016229 pairs aligned concordantly 0 times; of these: 207705 (6.89%) aligned discordantly 1 time ---- 2808524 pairs aligned 0 times concordantly or discordantly; of these: 5617048 mates make up the pairs; of these: 4771943 (84.95%) aligned 0 times 670954 (11.94%) aligned exactly 1 time 174151 (3.10%) aligned >1 times 94.59% overall alignment rate Time searching: 00:33:54 Overall time: 00:33:54 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 36 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] 29465697 / 41240105 = 0.7145 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 09:59:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.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 09:59:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:59:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:59:15: 1000000 INFO @ Tue, 16 Jun 2020 09:59:21: 2000000 INFO @ Tue, 16 Jun 2020 09:59:26: 3000000 INFO @ Tue, 16 Jun 2020 09:59:31: 4000000 INFO @ Tue, 16 Jun 2020 09:59:36: 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 09:59:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.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 09:59:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:59:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:59:42: 6000000 INFO @ Tue, 16 Jun 2020 09:59:45: 1000000 INFO @ Tue, 16 Jun 2020 09:59:47: 7000000 INFO @ Tue, 16 Jun 2020 09:59:51: 2000000 INFO @ Tue, 16 Jun 2020 09:59:52: 8000000 INFO @ Tue, 16 Jun 2020 09:59:56: 3000000 INFO @ Tue, 16 Jun 2020 09:59:57: 9000000 INFO @ Tue, 16 Jun 2020 10:00:01: 4000000 INFO @ Tue, 16 Jun 2020 10:00:03: 10000000 INFO @ Tue, 16 Jun 2020 10:00:07: 5000000 INFO @ Tue, 16 Jun 2020 10:00:08: 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 10:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.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 10:00:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:00:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:00:12: 6000000 INFO @ Tue, 16 Jun 2020 10:00:13: 12000000 INFO @ Tue, 16 Jun 2020 10:00:16: 1000000 INFO @ Tue, 16 Jun 2020 10:00:17: 7000000 INFO @ Tue, 16 Jun 2020 10:00:19: 13000000 INFO @ Tue, 16 Jun 2020 10:00:21: 2000000 INFO @ Tue, 16 Jun 2020 10:00:23: 8000000 INFO @ Tue, 16 Jun 2020 10:00:24: 14000000 INFO @ Tue, 16 Jun 2020 10:00:26: 3000000 INFO @ Tue, 16 Jun 2020 10:00:28: 9000000 INFO @ Tue, 16 Jun 2020 10:00:29: 15000000 INFO @ Tue, 16 Jun 2020 10:00:32: 4000000 INFO @ Tue, 16 Jun 2020 10:00:33: 10000000 INFO @ Tue, 16 Jun 2020 10:00:35: 16000000 INFO @ Tue, 16 Jun 2020 10:00:37: 5000000 INFO @ Tue, 16 Jun 2020 10:00:39: 11000000 INFO @ Tue, 16 Jun 2020 10:00:40: 17000000 INFO @ Tue, 16 Jun 2020 10:00:42: 6000000 INFO @ Tue, 16 Jun 2020 10:00:44: 12000000 INFO @ Tue, 16 Jun 2020 10:00:46: 18000000 INFO @ Tue, 16 Jun 2020 10:00:48: 7000000 INFO @ Tue, 16 Jun 2020 10:00:49: 13000000 INFO @ Tue, 16 Jun 2020 10:00:52: 19000000 INFO @ Tue, 16 Jun 2020 10:00:53: 8000000 INFO @ Tue, 16 Jun 2020 10:00:55: 14000000 INFO @ Tue, 16 Jun 2020 10:00:57: 20000000 INFO @ Tue, 16 Jun 2020 10:00:58: 9000000 INFO @ Tue, 16 Jun 2020 10:01:00: 15000000 INFO @ Tue, 16 Jun 2020 10:01:02: 21000000 INFO @ Tue, 16 Jun 2020 10:01:04: 10000000 INFO @ Tue, 16 Jun 2020 10:01:06: 16000000 INFO @ Tue, 16 Jun 2020 10:01:08: 22000000 INFO @ Tue, 16 Jun 2020 10:01:09: 11000000 INFO @ Tue, 16 Jun 2020 10:01:11: 17000000 INFO @ Tue, 16 Jun 2020 10:01:13: 23000000 INFO @ Tue, 16 Jun 2020 10:01:14: 12000000 INFO @ Tue, 16 Jun 2020 10:01:17: 18000000 INFO @ Tue, 16 Jun 2020 10:01:18: 24000000 INFO @ Tue, 16 Jun 2020 10:01:20: 13000000 INFO @ Tue, 16 Jun 2020 10:01:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:01:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:01:21: #1 total tags in treatment: 11731004 INFO @ Tue, 16 Jun 2020 10:01:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:21: #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 10:01:21: #1 tags after filtering in treatment: 9395092 INFO @ Tue, 16 Jun 2020 10:01:21: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 10:01:21: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:22: #2 number of paired peaks: 580 WARNING @ Tue, 16 Jun 2020 10:01:22: Fewer paired peaks (580) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 580 pairs to build model! INFO @ Tue, 16 Jun 2020 10:01:22: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:22: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:22: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:22: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:22: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 10:01:22: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 16 Jun 2020 10:01:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.05_model.r INFO @ Tue, 16 Jun 2020 10:01:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:01:22: 19000000 INFO @ Tue, 16 Jun 2020 10:01:25: 14000000 INFO @ Tue, 16 Jun 2020 10:01:27: 20000000 INFO @ Tue, 16 Jun 2020 10:01:30: 15000000 INFO @ Tue, 16 Jun 2020 10:01:33: 21000000 INFO @ Tue, 16 Jun 2020 10:01:35: 16000000 INFO @ Tue, 16 Jun 2020 10:01:39: 22000000 INFO @ Tue, 16 Jun 2020 10:01:41: 17000000 INFO @ Tue, 16 Jun 2020 10:01:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:01:44: 23000000 INFO @ Tue, 16 Jun 2020 10:01:46: 18000000 INFO @ Tue, 16 Jun 2020 10:01:49: 24000000 INFO @ Tue, 16 Jun 2020 10:01:52: 19000000 INFO @ Tue, 16 Jun 2020 10:01:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:01:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:01:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.05_summits.bed INFO @ Tue, 16 Jun 2020 10:01:52: Done! INFO @ Tue, 16 Jun 2020 10:01:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:01:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:01:52: #1 total tags in treatment: 11731004 INFO @ Tue, 16 Jun 2020 10:01:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:52: #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 10:01:52: #1 tags after filtering in treatment: 9395092 INFO @ Tue, 16 Jun 2020 10:01:52: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 10:01:52: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:53: #2 number of paired peaks: 580 WARNING @ Tue, 16 Jun 2020 10:01:53: Fewer paired peaks (580) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 580 pairs to build model! INFO @ Tue, 16 Jun 2020 10:01:53: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:53: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:53: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:53: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:53: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 10:01:53: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 16 Jun 2020 10:01:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.10_model.r INFO @ Tue, 16 Jun 2020 10:01:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:53: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2996 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:01:57: 20000000 INFO @ Tue, 16 Jun 2020 10:02:02: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:02:08: 22000000 INFO @ Tue, 16 Jun 2020 10:02:13: 23000000 INFO @ Tue, 16 Jun 2020 10:02:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:02:18: 24000000 INFO @ Tue, 16 Jun 2020 10:02:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:02:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:02:21: #1 total tags in treatment: 11731004 INFO @ Tue, 16 Jun 2020 10:02:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:02:21: #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 10:02:21: #1 tags after filtering in treatment: 9395092 INFO @ Tue, 16 Jun 2020 10:02:21: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 16 Jun 2020 10:02:21: #1 finished! INFO @ Tue, 16 Jun 2020 10:02:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:02:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:02:22: #2 number of paired peaks: 580 WARNING @ Tue, 16 Jun 2020 10:02:22: Fewer paired peaks (580) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 580 pairs to build model! INFO @ Tue, 16 Jun 2020 10:02:22: start model_add_line... INFO @ Tue, 16 Jun 2020 10:02:22: start X-correlation... INFO @ Tue, 16 Jun 2020 10:02:22: end of X-cor INFO @ Tue, 16 Jun 2020 10:02:22: #2 finished! INFO @ Tue, 16 Jun 2020 10:02:22: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 10:02:22: #2 alternative fragment length(s) may be 122 bps INFO @ Tue, 16 Jun 2020 10:02:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.20_model.r INFO @ Tue, 16 Jun 2020 10:02:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:02:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:02:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.10_summits.bed INFO @ Tue, 16 Jun 2020 10:02:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1870 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:02:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:02:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085395/SRX4085395.20_summits.bed INFO @ Tue, 16 Jun 2020 10:02:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (983 records, 4 fields): 3 millis CompletedMACS2peakCalling