Job ID = 14160466 SRX = SRX9555452 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:17:57 20936115 reads; of these: 20936115 (100.00%) were paired; of these: 1658525 (7.92%) aligned concordantly 0 times 16579301 (79.19%) aligned concordantly exactly 1 time 2698289 (12.89%) aligned concordantly >1 times ---- 1658525 pairs aligned concordantly 0 times; of these: 864785 (52.14%) aligned discordantly 1 time ---- 793740 pairs aligned 0 times concordantly or discordantly; of these: 1587480 mates make up the pairs; of these: 874347 (55.08%) aligned 0 times 453888 (28.59%) aligned exactly 1 time 259245 (16.33%) aligned >1 times 97.91% overall alignment rate Time searching: 00:17:57 Overall time: 00:17:57 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] 1293722 / 20132373 = 0.0643 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:07:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.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 @ Thu, 09 Dec 2021 03:07:01: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:01: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:06: 1000000 INFO @ Thu, 09 Dec 2021 03:07:11: 2000000 INFO @ Thu, 09 Dec 2021 03:07:16: 3000000 INFO @ Thu, 09 Dec 2021 03:07:21: 4000000 INFO @ Thu, 09 Dec 2021 03:07:26: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:07:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.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 @ Thu, 09 Dec 2021 03:07:31: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:31: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:32: 6000000 INFO @ Thu, 09 Dec 2021 03:07:36: 1000000 INFO @ Thu, 09 Dec 2021 03:07:37: 7000000 INFO @ Thu, 09 Dec 2021 03:07:41: 2000000 INFO @ Thu, 09 Dec 2021 03:07:42: 8000000 INFO @ Thu, 09 Dec 2021 03:07:45: 3000000 INFO @ Thu, 09 Dec 2021 03:07:48: 9000000 INFO @ Thu, 09 Dec 2021 03:07:50: 4000000 INFO @ Thu, 09 Dec 2021 03:07:53: 10000000 INFO @ Thu, 09 Dec 2021 03:07:54: 5000000 INFO @ Thu, 09 Dec 2021 03:07:58: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:07:59: 6000000 INFO @ Thu, 09 Dec 2021 03:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.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 @ Thu, 09 Dec 2021 03:08:00: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:08:00: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:08:03: 7000000 INFO @ Thu, 09 Dec 2021 03:08:04: 12000000 INFO @ Thu, 09 Dec 2021 03:08:05: 1000000 INFO @ Thu, 09 Dec 2021 03:08:08: 8000000 INFO @ Thu, 09 Dec 2021 03:08:09: 13000000 INFO @ Thu, 09 Dec 2021 03:08:10: 2000000 INFO @ Thu, 09 Dec 2021 03:08:12: 9000000 INFO @ Thu, 09 Dec 2021 03:08:15: 14000000 INFO @ Thu, 09 Dec 2021 03:08:16: 3000000 INFO @ Thu, 09 Dec 2021 03:08:17: 10000000 INFO @ Thu, 09 Dec 2021 03:08:20: 15000000 INFO @ Thu, 09 Dec 2021 03:08:21: 4000000 INFO @ Thu, 09 Dec 2021 03:08:22: 11000000 INFO @ Thu, 09 Dec 2021 03:08:25: 16000000 INFO @ Thu, 09 Dec 2021 03:08:26: 5000000 INFO @ Thu, 09 Dec 2021 03:08:26: 12000000 INFO @ Thu, 09 Dec 2021 03:08:30: 17000000 INFO @ Thu, 09 Dec 2021 03:08:31: 13000000 INFO @ Thu, 09 Dec 2021 03:08:31: 6000000 INFO @ Thu, 09 Dec 2021 03:08:35: 14000000 INFO @ Thu, 09 Dec 2021 03:08:36: 18000000 INFO @ Thu, 09 Dec 2021 03:08:37: 7000000 INFO @ Thu, 09 Dec 2021 03:08:40: 15000000 INFO @ Thu, 09 Dec 2021 03:08:41: 19000000 INFO @ Thu, 09 Dec 2021 03:08:42: 8000000 INFO @ Thu, 09 Dec 2021 03:08:44: 16000000 INFO @ Thu, 09 Dec 2021 03:08:47: 20000000 INFO @ Thu, 09 Dec 2021 03:08:48: 9000000 INFO @ Thu, 09 Dec 2021 03:08:49: 17000000 INFO @ Thu, 09 Dec 2021 03:08:52: 21000000 INFO @ Thu, 09 Dec 2021 03:08:53: 10000000 INFO @ Thu, 09 Dec 2021 03:08:53: 18000000 INFO @ Thu, 09 Dec 2021 03:08:57: 22000000 INFO @ Thu, 09 Dec 2021 03:08:58: 19000000 INFO @ Thu, 09 Dec 2021 03:08:58: 11000000 INFO @ Thu, 09 Dec 2021 03:09:02: 20000000 INFO @ Thu, 09 Dec 2021 03:09:03: 23000000 INFO @ Thu, 09 Dec 2021 03:09:04: 12000000 INFO @ Thu, 09 Dec 2021 03:09:07: 21000000 INFO @ Thu, 09 Dec 2021 03:09:08: 24000000 INFO @ Thu, 09 Dec 2021 03:09:09: 13000000 INFO @ Thu, 09 Dec 2021 03:09:11: 22000000 INFO @ Thu, 09 Dec 2021 03:09:13: 25000000 INFO @ Thu, 09 Dec 2021 03:09:14: 14000000 INFO @ Thu, 09 Dec 2021 03:09:16: 23000000 INFO @ Thu, 09 Dec 2021 03:09:19: 26000000 INFO @ Thu, 09 Dec 2021 03:09:20: 15000000 INFO @ Thu, 09 Dec 2021 03:09:20: 24000000 INFO @ Thu, 09 Dec 2021 03:09:24: 27000000 INFO @ Thu, 09 Dec 2021 03:09:25: 25000000 INFO @ Thu, 09 Dec 2021 03:09:25: 16000000 INFO @ Thu, 09 Dec 2021 03:09:29: 28000000 INFO @ Thu, 09 Dec 2021 03:09:29: 26000000 INFO @ Thu, 09 Dec 2021 03:09:30: 17000000 INFO @ Thu, 09 Dec 2021 03:09:34: 27000000 INFO @ Thu, 09 Dec 2021 03:09:35: 29000000 INFO @ Thu, 09 Dec 2021 03:09:36: 18000000 INFO @ Thu, 09 Dec 2021 03:09:38: 28000000 INFO @ Thu, 09 Dec 2021 03:09:40: 30000000 INFO @ Thu, 09 Dec 2021 03:09:41: 19000000 INFO @ Thu, 09 Dec 2021 03:09:42: 29000000 INFO @ Thu, 09 Dec 2021 03:09:45: 31000000 INFO @ Thu, 09 Dec 2021 03:09:46: 20000000 INFO @ Thu, 09 Dec 2021 03:09:47: 30000000 INFO @ Thu, 09 Dec 2021 03:09:51: 32000000 INFO @ Thu, 09 Dec 2021 03:09:52: 31000000 INFO @ Thu, 09 Dec 2021 03:09:52: 21000000 INFO @ Thu, 09 Dec 2021 03:09:56: 33000000 INFO @ Thu, 09 Dec 2021 03:09:56: 32000000 INFO @ Thu, 09 Dec 2021 03:09:57: 22000000 INFO @ Thu, 09 Dec 2021 03:10:01: 33000000 INFO @ Thu, 09 Dec 2021 03:10:01: 34000000 INFO @ Thu, 09 Dec 2021 03:10:02: 23000000 INFO @ Thu, 09 Dec 2021 03:10:05: 34000000 INFO @ Thu, 09 Dec 2021 03:10:07: 35000000 INFO @ Thu, 09 Dec 2021 03:10:08: 24000000 INFO @ Thu, 09 Dec 2021 03:10:10: 35000000 INFO @ Thu, 09 Dec 2021 03:10:12: 36000000 INFO @ Thu, 09 Dec 2021 03:10:13: 25000000 INFO @ Thu, 09 Dec 2021 03:10:14: 36000000 INFO @ Thu, 09 Dec 2021 03:10:17: 37000000 INFO @ Thu, 09 Dec 2021 03:10:18: 26000000 INFO @ Thu, 09 Dec 2021 03:10:19: 37000000 INFO @ Thu, 09 Dec 2021 03:10:23: 38000000 INFO @ Thu, 09 Dec 2021 03:10:23: 38000000 INFO @ Thu, 09 Dec 2021 03:10:24: 27000000 INFO @ Thu, 09 Dec 2021 03:10:25: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:10:25: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:10:25: #1 total tags in treatment: 18012820 INFO @ Thu, 09 Dec 2021 03:10:25: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:10:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:10:25: #1 tags after filtering in treatment: 16630426 INFO @ Thu, 09 Dec 2021 03:10:25: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 03:10:25: #1 finished! INFO @ Thu, 09 Dec 2021 03:10:25: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:10:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:10:26: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:10:26: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:10:26: #1 total tags in treatment: 18012820 INFO @ Thu, 09 Dec 2021 03:10:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:10:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:10:26: #1 tags after filtering in treatment: 16630426 INFO @ Thu, 09 Dec 2021 03:10:26: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 03:10:26: #1 finished! INFO @ Thu, 09 Dec 2021 03:10:26: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:10:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:10:27: #2 number of paired peaks: 290 WARNING @ Thu, 09 Dec 2021 03:10:27: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Thu, 09 Dec 2021 03:10:27: start model_add_line... INFO @ Thu, 09 Dec 2021 03:10:27: start X-correlation... INFO @ Thu, 09 Dec 2021 03:10:27: end of X-cor INFO @ Thu, 09 Dec 2021 03:10:27: #2 finished! INFO @ Thu, 09 Dec 2021 03:10:27: #2 predicted fragment length is 131 bps INFO @ Thu, 09 Dec 2021 03:10:27: #2 alternative fragment length(s) may be 3,103,131,146,159 bps INFO @ Thu, 09 Dec 2021 03:10:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.05_model.r INFO @ Thu, 09 Dec 2021 03:10:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:10:27: #2 number of paired peaks: 290 WARNING @ Thu, 09 Dec 2021 03:10:27: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Thu, 09 Dec 2021 03:10:27: start model_add_line... INFO @ Thu, 09 Dec 2021 03:10:27: start X-correlation... INFO @ Thu, 09 Dec 2021 03:10:27: end of X-cor INFO @ Thu, 09 Dec 2021 03:10:27: #2 finished! INFO @ Thu, 09 Dec 2021 03:10:27: #2 predicted fragment length is 131 bps INFO @ Thu, 09 Dec 2021 03:10:27: #2 alternative fragment length(s) may be 3,103,131,146,159 bps INFO @ Thu, 09 Dec 2021 03:10:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.10_model.r INFO @ Thu, 09 Dec 2021 03:10:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:10:29: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:10:34: 29000000 INFO @ Thu, 09 Dec 2021 03:10:40: 30000000 INFO @ Thu, 09 Dec 2021 03:10:45: 31000000 INFO @ Thu, 09 Dec 2021 03:10:50: 32000000 INFO @ Thu, 09 Dec 2021 03:10:55: 33000000 INFO @ Thu, 09 Dec 2021 03:10:56: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:10:57: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:11:00: 34000000 INFO @ Thu, 09 Dec 2021 03:11:06: 35000000 INFO @ Thu, 09 Dec 2021 03:11:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:11:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:11:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.05_summits.bed INFO @ Thu, 09 Dec 2021 03:11:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (454 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:11:11: 36000000 INFO @ Thu, 09 Dec 2021 03:11:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:11:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:11:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.10_summits.bed INFO @ Thu, 09 Dec 2021 03:11:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:11:16: 37000000 INFO @ Thu, 09 Dec 2021 03:11:21: 38000000 INFO @ Thu, 09 Dec 2021 03:11:24: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:11:24: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:11:24: #1 total tags in treatment: 18012820 INFO @ Thu, 09 Dec 2021 03:11:24: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:11:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:11:24: #1 tags after filtering in treatment: 16630426 INFO @ Thu, 09 Dec 2021 03:11:24: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 03:11:24: #1 finished! INFO @ Thu, 09 Dec 2021 03:11:24: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:11:25: #2 number of paired peaks: 290 WARNING @ Thu, 09 Dec 2021 03:11:25: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Thu, 09 Dec 2021 03:11:25: start model_add_line... INFO @ Thu, 09 Dec 2021 03:11:25: start X-correlation... INFO @ Thu, 09 Dec 2021 03:11:25: end of X-cor INFO @ Thu, 09 Dec 2021 03:11:25: #2 finished! INFO @ Thu, 09 Dec 2021 03:11:25: #2 predicted fragment length is 131 bps INFO @ Thu, 09 Dec 2021 03:11:25: #2 alternative fragment length(s) may be 3,103,131,146,159 bps INFO @ Thu, 09 Dec 2021 03:11:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.20_model.r INFO @ Thu, 09 Dec 2021 03:11:25: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:11:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:11:54: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:12:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:12:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:12:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555452/SRX9555452.20_summits.bed INFO @ Thu, 09 Dec 2021 03:12:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 3 millis CompletedMACS2peakCalling