Job ID = 12265571 SRX = SRX7687144 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:15:17 27010582 reads; of these: 27010582 (100.00%) were paired; of these: 5088101 (18.84%) aligned concordantly 0 times 14461938 (53.54%) aligned concordantly exactly 1 time 7460543 (27.62%) aligned concordantly >1 times ---- 5088101 pairs aligned concordantly 0 times; of these: 3689203 (72.51%) aligned discordantly 1 time ---- 1398898 pairs aligned 0 times concordantly or discordantly; of these: 2797796 mates make up the pairs; of these: 1188733 (42.49%) aligned 0 times 592864 (21.19%) aligned exactly 1 time 1016199 (36.32%) aligned >1 times 97.80% overall alignment rate Time searching: 01:15:18 Overall time: 01:15:18 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 24 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] 7779435 / 25565886 = 0.3043 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:10:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.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 @ Sat, 03 Apr 2021 09:10:40: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:10:40: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:10:45: 1000000 INFO @ Sat, 03 Apr 2021 09:10:51: 2000000 INFO @ Sat, 03 Apr 2021 09:10:57: 3000000 INFO @ Sat, 03 Apr 2021 09:11:02: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:11:08: 5000000 INFO @ Sat, 03 Apr 2021 09:11:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.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 @ Sat, 03 Apr 2021 09:11:10: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:11:10: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:11:13: 6000000 INFO @ Sat, 03 Apr 2021 09:11:16: 1000000 INFO @ Sat, 03 Apr 2021 09:11:19: 7000000 INFO @ Sat, 03 Apr 2021 09:11:22: 2000000 INFO @ Sat, 03 Apr 2021 09:11:25: 8000000 INFO @ Sat, 03 Apr 2021 09:11:28: 3000000 INFO @ Sat, 03 Apr 2021 09:11:31: 9000000 INFO @ Sat, 03 Apr 2021 09:11:34: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:11:37: 10000000 INFO @ Sat, 03 Apr 2021 09:11:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.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 @ Sat, 03 Apr 2021 09:11:40: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:11:40: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:11:40: 5000000 INFO @ Sat, 03 Apr 2021 09:11:44: 11000000 INFO @ Sat, 03 Apr 2021 09:11:47: 1000000 INFO @ Sat, 03 Apr 2021 09:11:47: 6000000 INFO @ Sat, 03 Apr 2021 09:11:51: 12000000 INFO @ Sat, 03 Apr 2021 09:11:54: 2000000 INFO @ Sat, 03 Apr 2021 09:11:54: 7000000 INFO @ Sat, 03 Apr 2021 09:11:58: 13000000 INFO @ Sat, 03 Apr 2021 09:12:00: 3000000 INFO @ Sat, 03 Apr 2021 09:12:01: 8000000 INFO @ Sat, 03 Apr 2021 09:12:05: 14000000 INFO @ Sat, 03 Apr 2021 09:12:07: 4000000 INFO @ Sat, 03 Apr 2021 09:12:08: 9000000 INFO @ Sat, 03 Apr 2021 09:12:11: 15000000 INFO @ Sat, 03 Apr 2021 09:12:14: 5000000 INFO @ Sat, 03 Apr 2021 09:12:15: 10000000 INFO @ Sat, 03 Apr 2021 09:12:18: 16000000 INFO @ Sat, 03 Apr 2021 09:12:21: 6000000 INFO @ Sat, 03 Apr 2021 09:12:22: 11000000 INFO @ Sat, 03 Apr 2021 09:12:25: 17000000 INFO @ Sat, 03 Apr 2021 09:12:28: 7000000 INFO @ Sat, 03 Apr 2021 09:12:29: 12000000 INFO @ Sat, 03 Apr 2021 09:12:32: 18000000 INFO @ Sat, 03 Apr 2021 09:12:35: 8000000 INFO @ Sat, 03 Apr 2021 09:12:36: 13000000 INFO @ Sat, 03 Apr 2021 09:12:38: 19000000 INFO @ Sat, 03 Apr 2021 09:12:42: 9000000 INFO @ Sat, 03 Apr 2021 09:12:43: 14000000 INFO @ Sat, 03 Apr 2021 09:12:46: 20000000 INFO @ Sat, 03 Apr 2021 09:12:49: 10000000 INFO @ Sat, 03 Apr 2021 09:12:50: 15000000 INFO @ Sat, 03 Apr 2021 09:12:53: 21000000 INFO @ Sat, 03 Apr 2021 09:12:57: 11000000 INFO @ Sat, 03 Apr 2021 09:12:57: 16000000 INFO @ Sat, 03 Apr 2021 09:12:59: 22000000 INFO @ Sat, 03 Apr 2021 09:13:04: 12000000 INFO @ Sat, 03 Apr 2021 09:13:04: 17000000 INFO @ Sat, 03 Apr 2021 09:13:06: 23000000 INFO @ Sat, 03 Apr 2021 09:13:11: 13000000 INFO @ Sat, 03 Apr 2021 09:13:11: 18000000 INFO @ Sat, 03 Apr 2021 09:13:13: 24000000 INFO @ Sat, 03 Apr 2021 09:13:18: 14000000 INFO @ Sat, 03 Apr 2021 09:13:19: 19000000 INFO @ Sat, 03 Apr 2021 09:13:20: 25000000 INFO @ Sat, 03 Apr 2021 09:13:26: 15000000 INFO @ Sat, 03 Apr 2021 09:13:26: 20000000 INFO @ Sat, 03 Apr 2021 09:13:27: 26000000 INFO @ Sat, 03 Apr 2021 09:13:33: 16000000 INFO @ Sat, 03 Apr 2021 09:13:33: 21000000 INFO @ Sat, 03 Apr 2021 09:13:34: 27000000 INFO @ Sat, 03 Apr 2021 09:13:40: 17000000 INFO @ Sat, 03 Apr 2021 09:13:40: 22000000 INFO @ Sat, 03 Apr 2021 09:13:41: 28000000 INFO @ Sat, 03 Apr 2021 09:13:47: 23000000 INFO @ Sat, 03 Apr 2021 09:13:47: 18000000 INFO @ Sat, 03 Apr 2021 09:13:47: 29000000 INFO @ Sat, 03 Apr 2021 09:13:53: 24000000 INFO @ Sat, 03 Apr 2021 09:13:53: 19000000 INFO @ Sat, 03 Apr 2021 09:13:54: 30000000 INFO @ Sat, 03 Apr 2021 09:14:00: 25000000 INFO @ Sat, 03 Apr 2021 09:14:01: 20000000 INFO @ Sat, 03 Apr 2021 09:14:01: 31000000 INFO @ Sat, 03 Apr 2021 09:14:07: 26000000 INFO @ Sat, 03 Apr 2021 09:14:07: 21000000 INFO @ Sat, 03 Apr 2021 09:14:08: 32000000 INFO @ Sat, 03 Apr 2021 09:14:14: 27000000 INFO @ Sat, 03 Apr 2021 09:14:14: 22000000 INFO @ Sat, 03 Apr 2021 09:14:14: 33000000 INFO @ Sat, 03 Apr 2021 09:14:20: 28000000 INFO @ Sat, 03 Apr 2021 09:14:21: 23000000 INFO @ Sat, 03 Apr 2021 09:14:21: 34000000 INFO @ Sat, 03 Apr 2021 09:14:27: 29000000 INFO @ Sat, 03 Apr 2021 09:14:27: 24000000 INFO @ Sat, 03 Apr 2021 09:14:27: 35000000 INFO @ Sat, 03 Apr 2021 09:14:34: 25000000 INFO @ Sat, 03 Apr 2021 09:14:34: 30000000 INFO @ Sat, 03 Apr 2021 09:14:34: 36000000 INFO @ Sat, 03 Apr 2021 09:14:40: 26000000 INFO @ Sat, 03 Apr 2021 09:14:40: 31000000 INFO @ Sat, 03 Apr 2021 09:14:40: 37000000 INFO @ Sat, 03 Apr 2021 09:14:42: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 09:14:42: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 09:14:42: #1 total tags in treatment: 14788175 INFO @ Sat, 03 Apr 2021 09:14:42: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:14:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:14:43: #1 tags after filtering in treatment: 10327361 INFO @ Sat, 03 Apr 2021 09:14:43: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 09:14:43: #1 finished! INFO @ Sat, 03 Apr 2021 09:14:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:14:43: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:14:43: #2 number of paired peaks: 475 WARNING @ Sat, 03 Apr 2021 09:14:43: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Sat, 03 Apr 2021 09:14:43: start model_add_line... INFO @ Sat, 03 Apr 2021 09:14:43: start X-correlation... INFO @ Sat, 03 Apr 2021 09:14:43: end of X-cor INFO @ Sat, 03 Apr 2021 09:14:43: #2 finished! INFO @ Sat, 03 Apr 2021 09:14:43: #2 predicted fragment length is 122 bps INFO @ Sat, 03 Apr 2021 09:14:43: #2 alternative fragment length(s) may be 3,108,122 bps INFO @ Sat, 03 Apr 2021 09:14:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.05_model.r WARNING @ Sat, 03 Apr 2021 09:14:43: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:14:43: #2 You may need to consider one of the other alternative d(s): 3,108,122 WARNING @ Sat, 03 Apr 2021 09:14:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:14:43: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:14:46: 27000000 INFO @ Sat, 03 Apr 2021 09:14:46: 32000000 INFO @ Sat, 03 Apr 2021 09:14:52: 28000000 INFO @ Sat, 03 Apr 2021 09:14:52: 33000000 INFO @ Sat, 03 Apr 2021 09:14:58: 29000000 INFO @ Sat, 03 Apr 2021 09:14:58: 34000000 INFO @ Sat, 03 Apr 2021 09:15:03: 30000000 INFO @ Sat, 03 Apr 2021 09:15:04: 35000000 INFO @ Sat, 03 Apr 2021 09:15:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:15:10: 31000000 INFO @ Sat, 03 Apr 2021 09:15:10: 36000000 INFO @ Sat, 03 Apr 2021 09:15:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:15:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:15:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.05_summits.bed INFO @ Sat, 03 Apr 2021 09:15:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (688 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:15:16: 32000000 INFO @ Sat, 03 Apr 2021 09:15:17: 37000000 INFO @ Sat, 03 Apr 2021 09:15:18: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 09:15:18: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 09:15:18: #1 total tags in treatment: 14788175 INFO @ Sat, 03 Apr 2021 09:15:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:15:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:15:19: #1 tags after filtering in treatment: 10327361 INFO @ Sat, 03 Apr 2021 09:15:19: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 09:15:19: #1 finished! INFO @ Sat, 03 Apr 2021 09:15:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:15:19: #2 number of paired peaks: 475 WARNING @ Sat, 03 Apr 2021 09:15:19: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Sat, 03 Apr 2021 09:15:19: start model_add_line... INFO @ Sat, 03 Apr 2021 09:15:19: start X-correlation... INFO @ Sat, 03 Apr 2021 09:15:19: end of X-cor INFO @ Sat, 03 Apr 2021 09:15:19: #2 finished! INFO @ Sat, 03 Apr 2021 09:15:19: #2 predicted fragment length is 122 bps INFO @ Sat, 03 Apr 2021 09:15:19: #2 alternative fragment length(s) may be 3,108,122 bps INFO @ Sat, 03 Apr 2021 09:15:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.10_model.r WARNING @ Sat, 03 Apr 2021 09:15:19: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:15:19: #2 You may need to consider one of the other alternative d(s): 3,108,122 WARNING @ Sat, 03 Apr 2021 09:15:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:15:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:15:22: 33000000 INFO @ Sat, 03 Apr 2021 09:15:27: 34000000 INFO @ Sat, 03 Apr 2021 09:15:33: 35000000 INFO @ Sat, 03 Apr 2021 09:15:38: 36000000 INFO @ Sat, 03 Apr 2021 09:15:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:15:44: 37000000 INFO @ Sat, 03 Apr 2021 09:15:45: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 09:15:45: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 09:15:45: #1 total tags in treatment: 14788175 INFO @ Sat, 03 Apr 2021 09:15:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:15:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:15:46: #1 tags after filtering in treatment: 10327361 INFO @ Sat, 03 Apr 2021 09:15:46: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 09:15:46: #1 finished! INFO @ Sat, 03 Apr 2021 09:15:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:15:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:15:46: #2 number of paired peaks: 475 WARNING @ Sat, 03 Apr 2021 09:15:46: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Sat, 03 Apr 2021 09:15:46: start model_add_line... INFO @ Sat, 03 Apr 2021 09:15:47: start X-correlation... INFO @ Sat, 03 Apr 2021 09:15:47: end of X-cor INFO @ Sat, 03 Apr 2021 09:15:47: #2 finished! INFO @ Sat, 03 Apr 2021 09:15:47: #2 predicted fragment length is 122 bps INFO @ Sat, 03 Apr 2021 09:15:47: #2 alternative fragment length(s) may be 3,108,122 bps INFO @ Sat, 03 Apr 2021 09:15:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.20_model.r WARNING @ Sat, 03 Apr 2021 09:15:47: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:15:47: #2 You may need to consider one of the other alternative d(s): 3,108,122 WARNING @ Sat, 03 Apr 2021 09:15:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:15:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:15:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:15:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:15:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:15:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.10_summits.bed INFO @ Sat, 03 Apr 2021 09:15:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (375 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:16:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:16:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:16:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:16:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687144/SRX7687144.20_summits.bed INFO @ Sat, 03 Apr 2021 09:16:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (206 records, 4 fields): 2 millis CompletedMACS2peakCalling