Job ID = 14159635 SRX = SRX8976692 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: 00:14:15 17389682 reads; of these: 17389682 (100.00%) were paired; of these: 1958951 (11.27%) aligned concordantly 0 times 12432870 (71.50%) aligned concordantly exactly 1 time 2997861 (17.24%) aligned concordantly >1 times ---- 1958951 pairs aligned concordantly 0 times; of these: 1206330 (61.58%) aligned discordantly 1 time ---- 752621 pairs aligned 0 times concordantly or discordantly; of these: 1505242 mates make up the pairs; of these: 534644 (35.52%) aligned 0 times 359649 (23.89%) aligned exactly 1 time 610949 (40.59%) aligned >1 times 98.46% overall alignment rate Time searching: 00:14:15 Overall time: 00:14:15 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 12 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] 1495488 / 16624680 = 0.0900 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 @ Wed, 08 Dec 2021 23:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.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 @ Wed, 08 Dec 2021 23:59:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:59:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:59:56: 1000000 INFO @ Thu, 09 Dec 2021 00:00:01: 2000000 INFO @ Thu, 09 Dec 2021 00:00:06: 3000000 INFO @ Thu, 09 Dec 2021 00:00:11: 4000000 INFO @ Thu, 09 Dec 2021 00:00:16: 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 00:00:20: 6000000 INFO @ Thu, 09 Dec 2021 00:00:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.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 00:00:21: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:00:21: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:00:26: 7000000 INFO @ Thu, 09 Dec 2021 00:00:27: 1000000 INFO @ Thu, 09 Dec 2021 00:00:31: 8000000 INFO @ Thu, 09 Dec 2021 00:00:32: 2000000 INFO @ Thu, 09 Dec 2021 00:00:37: 9000000 INFO @ Thu, 09 Dec 2021 00:00:38: 3000000 INFO @ Thu, 09 Dec 2021 00:00:42: 10000000 INFO @ Thu, 09 Dec 2021 00:00:43: 4000000 INFO @ Thu, 09 Dec 2021 00:00:48: 11000000 INFO @ Thu, 09 Dec 2021 00:00:49: 5000000 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 00:00:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.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 00:00:51: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:00:51: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:00:53: 12000000 INFO @ Thu, 09 Dec 2021 00:00:54: 6000000 INFO @ Thu, 09 Dec 2021 00:00:57: 1000000 INFO @ Thu, 09 Dec 2021 00:01:00: 13000000 INFO @ Thu, 09 Dec 2021 00:01:01: 7000000 INFO @ Thu, 09 Dec 2021 00:01:04: 2000000 INFO @ Thu, 09 Dec 2021 00:01:06: 14000000 INFO @ Thu, 09 Dec 2021 00:01:07: 8000000 INFO @ Thu, 09 Dec 2021 00:01:10: 3000000 INFO @ Thu, 09 Dec 2021 00:01:12: 15000000 INFO @ Thu, 09 Dec 2021 00:01:13: 9000000 INFO @ Thu, 09 Dec 2021 00:01:17: 4000000 INFO @ Thu, 09 Dec 2021 00:01:18: 16000000 INFO @ Thu, 09 Dec 2021 00:01:19: 10000000 INFO @ Thu, 09 Dec 2021 00:01:23: 5000000 INFO @ Thu, 09 Dec 2021 00:01:24: 17000000 INFO @ Thu, 09 Dec 2021 00:01:25: 11000000 INFO @ Thu, 09 Dec 2021 00:01:30: 6000000 INFO @ Thu, 09 Dec 2021 00:01:30: 18000000 INFO @ Thu, 09 Dec 2021 00:01:32: 12000000 INFO @ Thu, 09 Dec 2021 00:01:36: 7000000 INFO @ Thu, 09 Dec 2021 00:01:37: 19000000 INFO @ Thu, 09 Dec 2021 00:01:38: 13000000 INFO @ Thu, 09 Dec 2021 00:01:43: 20000000 INFO @ Thu, 09 Dec 2021 00:01:43: 8000000 INFO @ Thu, 09 Dec 2021 00:01:44: 14000000 INFO @ Thu, 09 Dec 2021 00:01:49: 21000000 INFO @ Thu, 09 Dec 2021 00:01:49: 9000000 INFO @ Thu, 09 Dec 2021 00:01:50: 15000000 INFO @ Thu, 09 Dec 2021 00:01:55: 22000000 INFO @ Thu, 09 Dec 2021 00:01:56: 10000000 INFO @ Thu, 09 Dec 2021 00:01:56: 16000000 INFO @ Thu, 09 Dec 2021 00:02:01: 23000000 INFO @ Thu, 09 Dec 2021 00:02:02: 11000000 INFO @ Thu, 09 Dec 2021 00:02:03: 17000000 INFO @ Thu, 09 Dec 2021 00:02:07: 24000000 INFO @ Thu, 09 Dec 2021 00:02:09: 18000000 INFO @ Thu, 09 Dec 2021 00:02:09: 12000000 INFO @ Thu, 09 Dec 2021 00:02:13: 25000000 INFO @ Thu, 09 Dec 2021 00:02:15: 19000000 INFO @ Thu, 09 Dec 2021 00:02:16: 13000000 INFO @ Thu, 09 Dec 2021 00:02:20: 26000000 INFO @ Thu, 09 Dec 2021 00:02:21: 20000000 INFO @ Thu, 09 Dec 2021 00:02:22: 14000000 INFO @ Thu, 09 Dec 2021 00:02:26: 27000000 INFO @ Thu, 09 Dec 2021 00:02:27: 21000000 INFO @ Thu, 09 Dec 2021 00:02:29: 15000000 INFO @ Thu, 09 Dec 2021 00:02:32: 28000000 INFO @ Thu, 09 Dec 2021 00:02:33: 22000000 INFO @ Thu, 09 Dec 2021 00:02:35: 16000000 INFO @ Thu, 09 Dec 2021 00:02:38: 29000000 INFO @ Thu, 09 Dec 2021 00:02:39: 23000000 INFO @ Thu, 09 Dec 2021 00:02:41: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:02:44: 30000000 INFO @ Thu, 09 Dec 2021 00:02:45: 24000000 INFO @ Thu, 09 Dec 2021 00:02:48: 18000000 INFO @ Thu, 09 Dec 2021 00:02:50: 31000000 INFO @ Thu, 09 Dec 2021 00:02:51: 25000000 INFO @ Thu, 09 Dec 2021 00:02:52: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:02:52: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:02:52: #1 total tags in treatment: 14012778 INFO @ Thu, 09 Dec 2021 00:02:52: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:02:52: #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 00:02:52: #1 tags after filtering in treatment: 12311096 INFO @ Thu, 09 Dec 2021 00:02:52: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 09 Dec 2021 00:02:52: #1 finished! INFO @ Thu, 09 Dec 2021 00:02:52: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:02:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:02:53: #2 number of paired peaks: 590 WARNING @ Thu, 09 Dec 2021 00:02:53: Fewer paired peaks (590) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 590 pairs to build model! INFO @ Thu, 09 Dec 2021 00:02:53: start model_add_line... INFO @ Thu, 09 Dec 2021 00:02:53: start X-correlation... INFO @ Thu, 09 Dec 2021 00:02:53: end of X-cor INFO @ Thu, 09 Dec 2021 00:02:53: #2 finished! INFO @ Thu, 09 Dec 2021 00:02:53: #2 predicted fragment length is 130 bps INFO @ Thu, 09 Dec 2021 00:02:53: #2 alternative fragment length(s) may be 3,130,145,149 bps INFO @ Thu, 09 Dec 2021 00:02:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.05_model.r INFO @ Thu, 09 Dec 2021 00:02:53: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:02:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:02:54: 19000000 INFO @ Thu, 09 Dec 2021 00:02:57: 26000000 INFO @ Thu, 09 Dec 2021 00:03:01: 20000000 INFO @ Thu, 09 Dec 2021 00:03:03: 27000000 INFO @ Thu, 09 Dec 2021 00:03:07: 21000000 INFO @ Thu, 09 Dec 2021 00:03:09: 28000000 INFO @ Thu, 09 Dec 2021 00:03:13: 22000000 INFO @ Thu, 09 Dec 2021 00:03:15: 29000000 INFO @ Thu, 09 Dec 2021 00:03:18: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:03:20: 23000000 INFO @ Thu, 09 Dec 2021 00:03:21: 30000000 INFO @ Thu, 09 Dec 2021 00:03:26: 24000000 INFO @ Thu, 09 Dec 2021 00:03:27: 31000000 INFO @ Thu, 09 Dec 2021 00:03:28: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:03:28: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:03:28: #1 total tags in treatment: 14012778 INFO @ Thu, 09 Dec 2021 00:03:28: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:03:28: #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 00:03:28: #1 tags after filtering in treatment: 12311096 INFO @ Thu, 09 Dec 2021 00:03:28: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 09 Dec 2021 00:03:28: #1 finished! INFO @ Thu, 09 Dec 2021 00:03:28: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:03:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:03:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:03:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.05_summits.bed INFO @ Thu, 09 Dec 2021 00:03:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (562 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:03:29: #2 number of paired peaks: 590 WARNING @ Thu, 09 Dec 2021 00:03:29: Fewer paired peaks (590) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 590 pairs to build model! INFO @ Thu, 09 Dec 2021 00:03:29: start model_add_line... INFO @ Thu, 09 Dec 2021 00:03:29: start X-correlation... INFO @ Thu, 09 Dec 2021 00:03:29: end of X-cor INFO @ Thu, 09 Dec 2021 00:03:29: #2 finished! INFO @ Thu, 09 Dec 2021 00:03:29: #2 predicted fragment length is 130 bps INFO @ Thu, 09 Dec 2021 00:03:29: #2 alternative fragment length(s) may be 3,130,145,149 bps INFO @ Thu, 09 Dec 2021 00:03:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.10_model.r INFO @ Thu, 09 Dec 2021 00:03:29: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:03:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:03:32: 25000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:03:38: 26000000 INFO @ Thu, 09 Dec 2021 00:03:44: 27000000 INFO @ Thu, 09 Dec 2021 00:03:50: 28000000 INFO @ Thu, 09 Dec 2021 00:03:54: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:03:55: 29000000 INFO @ Thu, 09 Dec 2021 00:04:01: 30000000 INFO @ Thu, 09 Dec 2021 00:04:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:04:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:04:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.10_summits.bed INFO @ Thu, 09 Dec 2021 00:04:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:04:07: 31000000 INFO @ Thu, 09 Dec 2021 00:04:08: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:04:08: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:04:08: #1 total tags in treatment: 14012778 INFO @ Thu, 09 Dec 2021 00:04:08: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:04:08: #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 00:04:09: #1 tags after filtering in treatment: 12311096 INFO @ Thu, 09 Dec 2021 00:04:09: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 09 Dec 2021 00:04:09: #1 finished! INFO @ Thu, 09 Dec 2021 00:04:09: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:04:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:04:09: #2 number of paired peaks: 590 WARNING @ Thu, 09 Dec 2021 00:04:09: Fewer paired peaks (590) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 590 pairs to build model! INFO @ Thu, 09 Dec 2021 00:04:09: start model_add_line... INFO @ Thu, 09 Dec 2021 00:04:10: start X-correlation... INFO @ Thu, 09 Dec 2021 00:04:10: end of X-cor INFO @ Thu, 09 Dec 2021 00:04:10: #2 finished! INFO @ Thu, 09 Dec 2021 00:04:10: #2 predicted fragment length is 130 bps INFO @ Thu, 09 Dec 2021 00:04:10: #2 alternative fragment length(s) may be 3,130,145,149 bps INFO @ Thu, 09 Dec 2021 00:04:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.20_model.r INFO @ Thu, 09 Dec 2021 00:04:10: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:04:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:04:33: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:04:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:04:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:04:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976692/SRX8976692.20_summits.bed INFO @ Thu, 09 Dec 2021 00:04:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 1 millis CompletedMACS2peakCalling