Job ID = 6368458 SRX = SRX4996815 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:26:46 prefetch.2.10.7: 1) Downloading 'SRR8176700'... 2020-06-16T00:26:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:16 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:16 prefetch.2.10.7: 1) 'SRR8176700' was downloaded successfully 2020-06-16T00:30:16 prefetch.2.10.7: 'SRR8176700' has 0 unresolved dependencies Read 22932478 spots for SRR8176700/SRR8176700.sra Written 22932478 spots for SRR8176700/SRR8176700.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: 00:20:17 22932478 reads; of these: 22932478 (100.00%) were paired; of these: 3309399 (14.43%) aligned concordantly 0 times 16700070 (72.82%) aligned concordantly exactly 1 time 2923009 (12.75%) aligned concordantly >1 times ---- 3309399 pairs aligned concordantly 0 times; of these: 2252252 (68.06%) aligned discordantly 1 time ---- 1057147 pairs aligned 0 times concordantly or discordantly; of these: 2114294 mates make up the pairs; of these: 903053 (42.71%) aligned 0 times 621382 (29.39%) aligned exactly 1 time 589859 (27.90%) aligned >1 times 98.03% overall alignment rate Time searching: 00:20:17 Overall time: 00:20:17 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] 612929 / 21855043 = 0.0280 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 10:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.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 10:04:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:04:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:04:10: 1000000 INFO @ Tue, 16 Jun 2020 10:04:17: 2000000 INFO @ Tue, 16 Jun 2020 10:04:24: 3000000 INFO @ Tue, 16 Jun 2020 10:04:30: 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 @ Tue, 16 Jun 2020 10:04:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.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 10:04:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:04:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:04:37: 5000000 INFO @ Tue, 16 Jun 2020 10:04:40: 1000000 INFO @ Tue, 16 Jun 2020 10:04:45: 6000000 INFO @ Tue, 16 Jun 2020 10:04:47: 2000000 INFO @ Tue, 16 Jun 2020 10:04:52: 7000000 INFO @ Tue, 16 Jun 2020 10:04:54: 3000000 INFO @ Tue, 16 Jun 2020 10:04:59: 8000000 INFO @ Tue, 16 Jun 2020 10:05:01: 4000000 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 10:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.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 10:05:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:05:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:05:06: 9000000 INFO @ Tue, 16 Jun 2020 10:05:08: 5000000 INFO @ Tue, 16 Jun 2020 10:05:11: 1000000 INFO @ Tue, 16 Jun 2020 10:05:14: 10000000 INFO @ Tue, 16 Jun 2020 10:05:15: 6000000 INFO @ Tue, 16 Jun 2020 10:05:18: 2000000 INFO @ Tue, 16 Jun 2020 10:05:21: 11000000 INFO @ Tue, 16 Jun 2020 10:05:22: 7000000 INFO @ Tue, 16 Jun 2020 10:05:25: 3000000 INFO @ Tue, 16 Jun 2020 10:05:29: 12000000 INFO @ Tue, 16 Jun 2020 10:05:29: 8000000 INFO @ Tue, 16 Jun 2020 10:05:33: 4000000 INFO @ Tue, 16 Jun 2020 10:05:36: 13000000 INFO @ Tue, 16 Jun 2020 10:05:36: 9000000 INFO @ Tue, 16 Jun 2020 10:05:40: 5000000 INFO @ Tue, 16 Jun 2020 10:05:43: 10000000 INFO @ Tue, 16 Jun 2020 10:05:44: 14000000 INFO @ Tue, 16 Jun 2020 10:05:47: 6000000 INFO @ Tue, 16 Jun 2020 10:05:50: 11000000 INFO @ Tue, 16 Jun 2020 10:05:51: 15000000 INFO @ Tue, 16 Jun 2020 10:05:54: 7000000 INFO @ Tue, 16 Jun 2020 10:05:58: 12000000 INFO @ Tue, 16 Jun 2020 10:05:59: 16000000 INFO @ Tue, 16 Jun 2020 10:06:01: 8000000 INFO @ Tue, 16 Jun 2020 10:06:05: 13000000 INFO @ Tue, 16 Jun 2020 10:06:06: 17000000 INFO @ Tue, 16 Jun 2020 10:06:09: 9000000 INFO @ Tue, 16 Jun 2020 10:06:12: 14000000 INFO @ Tue, 16 Jun 2020 10:06:14: 18000000 INFO @ Tue, 16 Jun 2020 10:06:16: 10000000 INFO @ Tue, 16 Jun 2020 10:06:19: 15000000 INFO @ Tue, 16 Jun 2020 10:06:21: 19000000 INFO @ Tue, 16 Jun 2020 10:06:23: 11000000 INFO @ Tue, 16 Jun 2020 10:06:26: 16000000 INFO @ Tue, 16 Jun 2020 10:06:29: 20000000 INFO @ Tue, 16 Jun 2020 10:06:30: 12000000 INFO @ Tue, 16 Jun 2020 10:06:33: 17000000 INFO @ Tue, 16 Jun 2020 10:06:37: 21000000 INFO @ Tue, 16 Jun 2020 10:06:38: 13000000 INFO @ Tue, 16 Jun 2020 10:06:40: 18000000 INFO @ Tue, 16 Jun 2020 10:06:44: 22000000 INFO @ Tue, 16 Jun 2020 10:06:45: 14000000 INFO @ Tue, 16 Jun 2020 10:06:47: 19000000 INFO @ Tue, 16 Jun 2020 10:06:52: 23000000 INFO @ Tue, 16 Jun 2020 10:06:52: 15000000 INFO @ Tue, 16 Jun 2020 10:06:54: 20000000 INFO @ Tue, 16 Jun 2020 10:06:59: 24000000 INFO @ Tue, 16 Jun 2020 10:07:00: 16000000 INFO @ Tue, 16 Jun 2020 10:07:02: 21000000 INFO @ Tue, 16 Jun 2020 10:07:07: 25000000 INFO @ Tue, 16 Jun 2020 10:07:07: 17000000 INFO @ Tue, 16 Jun 2020 10:07:09: 22000000 INFO @ Tue, 16 Jun 2020 10:07:14: 18000000 INFO @ Tue, 16 Jun 2020 10:07:14: 26000000 INFO @ Tue, 16 Jun 2020 10:07:16: 23000000 INFO @ Tue, 16 Jun 2020 10:07:21: 19000000 INFO @ Tue, 16 Jun 2020 10:07:21: 27000000 INFO @ Tue, 16 Jun 2020 10:07:23: 24000000 INFO @ Tue, 16 Jun 2020 10:07:28: 20000000 INFO @ Tue, 16 Jun 2020 10:07:29: 28000000 INFO @ Tue, 16 Jun 2020 10:07:30: 25000000 INFO @ Tue, 16 Jun 2020 10:07:35: 21000000 INFO @ Tue, 16 Jun 2020 10:07:36: 29000000 INFO @ Tue, 16 Jun 2020 10:07:37: 26000000 INFO @ Tue, 16 Jun 2020 10:07:42: 22000000 INFO @ Tue, 16 Jun 2020 10:07:44: 27000000 INFO @ Tue, 16 Jun 2020 10:07:44: 30000000 INFO @ Tue, 16 Jun 2020 10:07:50: 23000000 INFO @ Tue, 16 Jun 2020 10:07:51: 28000000 INFO @ Tue, 16 Jun 2020 10:07:51: 31000000 INFO @ Tue, 16 Jun 2020 10:07:57: 24000000 INFO @ Tue, 16 Jun 2020 10:07:58: 29000000 INFO @ Tue, 16 Jun 2020 10:07:59: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:08:04: 25000000 INFO @ Tue, 16 Jun 2020 10:08:05: 30000000 INFO @ Tue, 16 Jun 2020 10:08:06: 33000000 INFO @ Tue, 16 Jun 2020 10:08:11: 26000000 INFO @ Tue, 16 Jun 2020 10:08:12: 31000000 INFO @ Tue, 16 Jun 2020 10:08:14: 34000000 INFO @ Tue, 16 Jun 2020 10:08:18: 27000000 INFO @ Tue, 16 Jun 2020 10:08:19: 32000000 INFO @ Tue, 16 Jun 2020 10:08:21: 35000000 INFO @ Tue, 16 Jun 2020 10:08:25: 28000000 INFO @ Tue, 16 Jun 2020 10:08:26: 33000000 INFO @ Tue, 16 Jun 2020 10:08:28: 36000000 INFO @ Tue, 16 Jun 2020 10:08:32: 29000000 INFO @ Tue, 16 Jun 2020 10:08:33: 34000000 INFO @ Tue, 16 Jun 2020 10:08:35: 37000000 INFO @ Tue, 16 Jun 2020 10:08:39: 30000000 INFO @ Tue, 16 Jun 2020 10:08:40: 35000000 INFO @ Tue, 16 Jun 2020 10:08:42: 38000000 INFO @ Tue, 16 Jun 2020 10:08:46: 31000000 INFO @ Tue, 16 Jun 2020 10:08:47: 36000000 INFO @ Tue, 16 Jun 2020 10:08:50: 39000000 INFO @ Tue, 16 Jun 2020 10:08:53: 32000000 INFO @ Tue, 16 Jun 2020 10:08:54: 37000000 INFO @ Tue, 16 Jun 2020 10:08:57: 40000000 INFO @ Tue, 16 Jun 2020 10:09:00: 33000000 INFO @ Tue, 16 Jun 2020 10:09:02: 38000000 INFO @ Tue, 16 Jun 2020 10:09:04: 41000000 INFO @ Tue, 16 Jun 2020 10:09:08: 34000000 INFO @ Tue, 16 Jun 2020 10:09:09: 39000000 INFO @ Tue, 16 Jun 2020 10:09:11: 42000000 INFO @ Tue, 16 Jun 2020 10:09:15: 35000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:09:16: 40000000 INFO @ Tue, 16 Jun 2020 10:09:18: 43000000 INFO @ Tue, 16 Jun 2020 10:09:22: 36000000 INFO @ Tue, 16 Jun 2020 10:09:23: 41000000 INFO @ Tue, 16 Jun 2020 10:09:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:09:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:09:23: #1 total tags in treatment: 19038154 INFO @ Tue, 16 Jun 2020 10:09:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:09:23: #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 10:09:24: #1 tags after filtering in treatment: 17143173 INFO @ Tue, 16 Jun 2020 10:09:24: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 10:09:24: #1 finished! INFO @ Tue, 16 Jun 2020 10:09:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:09:25: #2 number of paired peaks: 318 WARNING @ Tue, 16 Jun 2020 10:09:25: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 16 Jun 2020 10:09:25: start model_add_line... INFO @ Tue, 16 Jun 2020 10:09:25: start X-correlation... INFO @ Tue, 16 Jun 2020 10:09:25: end of X-cor INFO @ Tue, 16 Jun 2020 10:09:25: #2 finished! INFO @ Tue, 16 Jun 2020 10:09:25: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 10:09:25: #2 alternative fragment length(s) may be 3,122,143 bps INFO @ Tue, 16 Jun 2020 10:09:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.05_model.r INFO @ Tue, 16 Jun 2020 10:09:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:09:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:09:29: 37000000 INFO @ Tue, 16 Jun 2020 10:09:30: 42000000 INFO @ Tue, 16 Jun 2020 10:09:35: 38000000 INFO @ Tue, 16 Jun 2020 10:09:36: 43000000 INFO @ Tue, 16 Jun 2020 10:09:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:09:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:09:41: #1 total tags in treatment: 19038154 INFO @ Tue, 16 Jun 2020 10:09:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:09:41: #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 10:09:41: #1 tags after filtering in treatment: 17143173 INFO @ Tue, 16 Jun 2020 10:09:41: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 10:09:41: #1 finished! INFO @ Tue, 16 Jun 2020 10:09:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:09:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:09:41: 39000000 INFO @ Tue, 16 Jun 2020 10:09:43: #2 number of paired peaks: 318 WARNING @ Tue, 16 Jun 2020 10:09:43: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 16 Jun 2020 10:09:43: start model_add_line... INFO @ Tue, 16 Jun 2020 10:09:43: start X-correlation... INFO @ Tue, 16 Jun 2020 10:09:43: end of X-cor INFO @ Tue, 16 Jun 2020 10:09:43: #2 finished! INFO @ Tue, 16 Jun 2020 10:09:43: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 10:09:43: #2 alternative fragment length(s) may be 3,122,143 bps INFO @ Tue, 16 Jun 2020 10:09:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.10_model.r INFO @ Tue, 16 Jun 2020 10:09:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:09:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:09:47: 40000000 INFO @ Tue, 16 Jun 2020 10:09:53: 41000000 INFO @ Tue, 16 Jun 2020 10:09:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:09:59: 42000000 INFO @ Tue, 16 Jun 2020 10:10:05: 43000000 INFO @ Tue, 16 Jun 2020 10:10:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:10:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:10:09: #1 total tags in treatment: 19038154 INFO @ Tue, 16 Jun 2020 10:10:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:10:09: #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 10:10:09: #1 tags after filtering in treatment: 17143173 INFO @ Tue, 16 Jun 2020 10:10:09: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 10:10:09: #1 finished! INFO @ Tue, 16 Jun 2020 10:10:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:10:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:10:10: #2 number of paired peaks: 318 WARNING @ Tue, 16 Jun 2020 10:10:10: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 16 Jun 2020 10:10:10: start model_add_line... INFO @ Tue, 16 Jun 2020 10:10:10: start X-correlation... INFO @ Tue, 16 Jun 2020 10:10:10: end of X-cor INFO @ Tue, 16 Jun 2020 10:10:10: #2 finished! INFO @ Tue, 16 Jun 2020 10:10:10: #2 predicted fragment length is 122 bps INFO @ Tue, 16 Jun 2020 10:10:10: #2 alternative fragment length(s) may be 3,122,143 bps INFO @ Tue, 16 Jun 2020 10:10:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.20_model.r INFO @ Tue, 16 Jun 2020 10:10:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:10:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:10:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:10:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:10:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.05_summits.bed INFO @ Tue, 16 Jun 2020 10:10:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:10:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:10:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:10:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:10:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.10_summits.bed INFO @ Tue, 16 Jun 2020 10:10:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:10:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:10:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:10:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:10:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996815/SRX4996815.20_summits.bed INFO @ Tue, 16 Jun 2020 10:10:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (225 records, 4 fields): 1 millis CompletedMACS2peakCalling