Job ID = 6367201 SRX = SRX2978705 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:18:16 prefetch.2.10.7: 1) Downloading 'SRR5799212'... 2020-06-15T23:18:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:20:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:20:18 prefetch.2.10.7: 1) 'SRR5799212' was downloaded successfully 2020-06-15T23:20:19 prefetch.2.10.7: 'SRR5799212' has 0 unresolved dependencies Read 21248963 spots for SRR5799212/SRR5799212.sra Written 21248963 spots for SRR5799212/SRR5799212.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: 00:17:54 21248963 reads; of these: 21248963 (100.00%) were paired; of these: 1226531 (5.77%) aligned concordantly 0 times 17217714 (81.03%) aligned concordantly exactly 1 time 2804718 (13.20%) aligned concordantly >1 times ---- 1226531 pairs aligned concordantly 0 times; of these: 702613 (57.28%) aligned discordantly 1 time ---- 523918 pairs aligned 0 times concordantly or discordantly; of these: 1047836 mates make up the pairs; of these: 602958 (57.54%) aligned 0 times 261220 (24.93%) aligned exactly 1 time 183658 (17.53%) aligned >1 times 98.58% overall alignment rate Time searching: 00:17:54 Overall time: 00:17:54 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 20 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] 358995 / 20714359 = 0.0173 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 08:50:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.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 08:50:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:37: 1000000 INFO @ Tue, 16 Jun 2020 08:50:42: 2000000 INFO @ Tue, 16 Jun 2020 08:50:46: 3000000 INFO @ Tue, 16 Jun 2020 08:50:51: 4000000 INFO @ Tue, 16 Jun 2020 08:50:55: 5000000 INFO @ Tue, 16 Jun 2020 08:50:59: 6000000 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 08:51:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.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 08:51:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:04: 7000000 INFO @ Tue, 16 Jun 2020 08:51:08: 1000000 INFO @ Tue, 16 Jun 2020 08:51:09: 8000000 INFO @ Tue, 16 Jun 2020 08:51:14: 9000000 INFO @ Tue, 16 Jun 2020 08:51:14: 2000000 INFO @ Tue, 16 Jun 2020 08:51:18: 10000000 INFO @ Tue, 16 Jun 2020 08:51:19: 3000000 INFO @ Tue, 16 Jun 2020 08:51:23: 11000000 INFO @ Tue, 16 Jun 2020 08:51:24: 4000000 INFO @ Tue, 16 Jun 2020 08:51:28: 12000000 INFO @ Tue, 16 Jun 2020 08:51:30: 5000000 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 08:51:32: 13000000 INFO @ Tue, 16 Jun 2020 08:51:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.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 08:51:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:35: 6000000 INFO @ Tue, 16 Jun 2020 08:51:37: 14000000 INFO @ Tue, 16 Jun 2020 08:51:39: 1000000 INFO @ Tue, 16 Jun 2020 08:51:41: 7000000 INFO @ Tue, 16 Jun 2020 08:51:42: 15000000 INFO @ Tue, 16 Jun 2020 08:51:44: 2000000 INFO @ Tue, 16 Jun 2020 08:51:46: 8000000 INFO @ Tue, 16 Jun 2020 08:51:47: 16000000 INFO @ Tue, 16 Jun 2020 08:51:50: 3000000 INFO @ Tue, 16 Jun 2020 08:51:51: 17000000 INFO @ Tue, 16 Jun 2020 08:51:52: 9000000 INFO @ Tue, 16 Jun 2020 08:51:55: 4000000 INFO @ Tue, 16 Jun 2020 08:51:56: 18000000 INFO @ Tue, 16 Jun 2020 08:51:57: 10000000 INFO @ Tue, 16 Jun 2020 08:52:01: 19000000 INFO @ Tue, 16 Jun 2020 08:52:01: 5000000 INFO @ Tue, 16 Jun 2020 08:52:03: 11000000 INFO @ Tue, 16 Jun 2020 08:52:05: 20000000 INFO @ Tue, 16 Jun 2020 08:52:07: 6000000 INFO @ Tue, 16 Jun 2020 08:52:08: 12000000 INFO @ Tue, 16 Jun 2020 08:52:10: 21000000 INFO @ Tue, 16 Jun 2020 08:52:12: 7000000 INFO @ Tue, 16 Jun 2020 08:52:14: 13000000 INFO @ Tue, 16 Jun 2020 08:52:14: 22000000 INFO @ Tue, 16 Jun 2020 08:52:18: 8000000 INFO @ Tue, 16 Jun 2020 08:52:19: 23000000 INFO @ Tue, 16 Jun 2020 08:52:19: 14000000 INFO @ Tue, 16 Jun 2020 08:52:24: 24000000 INFO @ Tue, 16 Jun 2020 08:52:24: 9000000 INFO @ Tue, 16 Jun 2020 08:52:25: 15000000 INFO @ Tue, 16 Jun 2020 08:52:28: 25000000 INFO @ Tue, 16 Jun 2020 08:52:30: 10000000 INFO @ Tue, 16 Jun 2020 08:52:30: 16000000 INFO @ Tue, 16 Jun 2020 08:52:33: 26000000 INFO @ Tue, 16 Jun 2020 08:52:35: 11000000 INFO @ Tue, 16 Jun 2020 08:52:36: 17000000 INFO @ Tue, 16 Jun 2020 08:52:38: 27000000 INFO @ Tue, 16 Jun 2020 08:52:41: 12000000 INFO @ Tue, 16 Jun 2020 08:52:42: 18000000 INFO @ Tue, 16 Jun 2020 08:52:43: 28000000 INFO @ Tue, 16 Jun 2020 08:52:47: 13000000 INFO @ Tue, 16 Jun 2020 08:52:47: 19000000 INFO @ Tue, 16 Jun 2020 08:52:48: 29000000 INFO @ Tue, 16 Jun 2020 08:52:52: 30000000 INFO @ Tue, 16 Jun 2020 08:52:53: 14000000 INFO @ Tue, 16 Jun 2020 08:52:53: 20000000 INFO @ Tue, 16 Jun 2020 08:52:57: 31000000 INFO @ Tue, 16 Jun 2020 08:52:59: 21000000 INFO @ Tue, 16 Jun 2020 08:52:59: 15000000 INFO @ Tue, 16 Jun 2020 08:53:02: 32000000 INFO @ Tue, 16 Jun 2020 08:53:05: 22000000 INFO @ Tue, 16 Jun 2020 08:53:05: 16000000 INFO @ Tue, 16 Jun 2020 08:53:07: 33000000 INFO @ Tue, 16 Jun 2020 08:53:11: 23000000 INFO @ Tue, 16 Jun 2020 08:53:11: 17000000 INFO @ Tue, 16 Jun 2020 08:53:12: 34000000 INFO @ Tue, 16 Jun 2020 08:53:16: 24000000 INFO @ Tue, 16 Jun 2020 08:53:17: 18000000 INFO @ Tue, 16 Jun 2020 08:53:17: 35000000 INFO @ Tue, 16 Jun 2020 08:53:22: 36000000 INFO @ Tue, 16 Jun 2020 08:53:22: 25000000 INFO @ Tue, 16 Jun 2020 08:53:23: 19000000 INFO @ Tue, 16 Jun 2020 08:53:27: 37000000 INFO @ Tue, 16 Jun 2020 08:53:28: 26000000 INFO @ Tue, 16 Jun 2020 08:53:29: 20000000 INFO @ Tue, 16 Jun 2020 08:53:32: 38000000 INFO @ Tue, 16 Jun 2020 08:53:34: 27000000 INFO @ Tue, 16 Jun 2020 08:53:35: 21000000 INFO @ Tue, 16 Jun 2020 08:53:37: 39000000 INFO @ Tue, 16 Jun 2020 08:53:40: 28000000 INFO @ Tue, 16 Jun 2020 08:53:41: 22000000 INFO @ Tue, 16 Jun 2020 08:53:42: 40000000 INFO @ Tue, 16 Jun 2020 08:53:46: 29000000 INFO @ Tue, 16 Jun 2020 08:53:47: 41000000 INFO @ Tue, 16 Jun 2020 08:53:47: 23000000 INFO @ Tue, 16 Jun 2020 08:53:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:53:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:53:48: #1 total tags in treatment: 19667743 INFO @ Tue, 16 Jun 2020 08:53:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:48: #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 08:53:48: #1 tags after filtering in treatment: 17629588 INFO @ Tue, 16 Jun 2020 08:53:48: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:53:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:50: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 08:53:50: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 08:53:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:50: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 08:53:50: #2 alternative fragment length(s) may be 4,106,131 bps INFO @ Tue, 16 Jun 2020 08:53:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.05_model.r INFO @ Tue, 16 Jun 2020 08:53:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:53:52: 30000000 INFO @ Tue, 16 Jun 2020 08:53:53: 24000000 INFO @ Tue, 16 Jun 2020 08:53:58: 31000000 INFO @ Tue, 16 Jun 2020 08:53:59: 25000000 INFO @ Tue, 16 Jun 2020 08:54:04: 32000000 INFO @ Tue, 16 Jun 2020 08:54:05: 26000000 INFO @ Tue, 16 Jun 2020 08:54:10: 33000000 INFO @ Tue, 16 Jun 2020 08:54:11: 27000000 INFO @ Tue, 16 Jun 2020 08:54:16: 34000000 INFO @ Tue, 16 Jun 2020 08:54:17: 28000000 INFO @ Tue, 16 Jun 2020 08:54:22: 35000000 INFO @ Tue, 16 Jun 2020 08:54:23: 29000000 INFO @ Tue, 16 Jun 2020 08:54:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:54:28: 36000000 INFO @ Tue, 16 Jun 2020 08:54:29: 30000000 INFO @ Tue, 16 Jun 2020 08:54:34: 37000000 INFO @ Tue, 16 Jun 2020 08:54:35: 31000000 INFO @ Tue, 16 Jun 2020 08:54:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:54:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:54:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.05_summits.bed INFO @ Tue, 16 Jun 2020 08:54:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (514 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:54:40: 38000000 INFO @ Tue, 16 Jun 2020 08:54:41: 32000000 INFO @ Tue, 16 Jun 2020 08:54:46: 39000000 INFO @ Tue, 16 Jun 2020 08:54:48: 33000000 INFO @ Tue, 16 Jun 2020 08:54:52: 40000000 INFO @ Tue, 16 Jun 2020 08:54:53: 34000000 INFO @ Tue, 16 Jun 2020 08:54:58: 41000000 INFO @ Tue, 16 Jun 2020 08:54:59: 35000000 INFO @ Tue, 16 Jun 2020 08:55:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:55:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:55:00: #1 total tags in treatment: 19667743 INFO @ Tue, 16 Jun 2020 08:55:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:00: #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 08:55:00: #1 tags after filtering in treatment: 17629588 INFO @ Tue, 16 Jun 2020 08:55:00: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:55:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:01: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 08:55:01: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:01: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 08:55:01: #2 alternative fragment length(s) may be 4,106,131 bps INFO @ Tue, 16 Jun 2020 08:55:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.10_model.r INFO @ Tue, 16 Jun 2020 08:55:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:05: 36000000 INFO @ Tue, 16 Jun 2020 08:55:11: 37000000 INFO @ Tue, 16 Jun 2020 08:55:17: 38000000 INFO @ Tue, 16 Jun 2020 08:55:22: 39000000 INFO @ Tue, 16 Jun 2020 08:55:28: 40000000 INFO @ Tue, 16 Jun 2020 08:55:34: 41000000 INFO @ Tue, 16 Jun 2020 08:55:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:55:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:55:35: #1 total tags in treatment: 19667743 INFO @ Tue, 16 Jun 2020 08:55:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:35: #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 08:55:35: #1 tags after filtering in treatment: 17629588 INFO @ Tue, 16 Jun 2020 08:55:35: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 08:55:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:37: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 08:55:37: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:55:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:37: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 08:55:37: #2 alternative fragment length(s) may be 4,106,131 bps INFO @ Tue, 16 Jun 2020 08:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.20_model.r INFO @ Tue, 16 Jun 2020 08:55:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:55:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:55:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:55:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.10_summits.bed INFO @ Tue, 16 Jun 2020 08:55:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (391 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:56:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978705/SRX2978705.20_summits.bed INFO @ Tue, 16 Jun 2020 08:56:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 4 millis CompletedMACS2peakCalling