Job ID = 12265497 SRX = SRX7687151 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: 00:42:13 32752234 reads; of these: 32752234 (100.00%) were paired; of these: 7634189 (23.31%) aligned concordantly 0 times 20663293 (63.09%) aligned concordantly exactly 1 time 4454752 (13.60%) aligned concordantly >1 times ---- 7634189 pairs aligned concordantly 0 times; of these: 5047098 (66.11%) aligned discordantly 1 time ---- 2587091 pairs aligned 0 times concordantly or discordantly; of these: 5174182 mates make up the pairs; of these: 3049423 (58.94%) aligned 0 times 788281 (15.23%) aligned exactly 1 time 1336478 (25.83%) aligned >1 times 95.34% overall alignment rate Time searching: 00:42:13 Overall time: 00:42:13 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 28 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] 13275674 / 30130563 = 0.4406 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 08:13:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.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 08:13:21: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:13:21: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:13:27: 1000000 INFO @ Sat, 03 Apr 2021 08:13:33: 2000000 INFO @ Sat, 03 Apr 2021 08:13:39: 3000000 INFO @ Sat, 03 Apr 2021 08:13:45: 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 08:13:50: 5000000 INFO @ Sat, 03 Apr 2021 08:13:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.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 08:13:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:13:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:13:57: 6000000 INFO @ Sat, 03 Apr 2021 08:13:58: 1000000 INFO @ Sat, 03 Apr 2021 08:14:03: 7000000 INFO @ Sat, 03 Apr 2021 08:14:05: 2000000 INFO @ Sat, 03 Apr 2021 08:14:09: 8000000 INFO @ Sat, 03 Apr 2021 08:14:11: 3000000 INFO @ Sat, 03 Apr 2021 08:14:15: 9000000 INFO @ Sat, 03 Apr 2021 08:14:18: 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 08:14:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.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 08:14:21: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:14:21: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:14:22: 10000000 INFO @ Sat, 03 Apr 2021 08:14:24: 5000000 INFO @ Sat, 03 Apr 2021 08:14:28: 1000000 INFO @ Sat, 03 Apr 2021 08:14:28: 11000000 INFO @ Sat, 03 Apr 2021 08:14:31: 6000000 INFO @ Sat, 03 Apr 2021 08:14:34: 2000000 INFO @ Sat, 03 Apr 2021 08:14:35: 12000000 INFO @ Sat, 03 Apr 2021 08:14:38: 7000000 INFO @ Sat, 03 Apr 2021 08:14:41: 3000000 INFO @ Sat, 03 Apr 2021 08:14:41: 13000000 INFO @ Sat, 03 Apr 2021 08:14:44: 8000000 INFO @ Sat, 03 Apr 2021 08:14:47: 4000000 INFO @ Sat, 03 Apr 2021 08:14:48: 14000000 INFO @ Sat, 03 Apr 2021 08:14:51: 9000000 INFO @ Sat, 03 Apr 2021 08:14:53: 5000000 INFO @ Sat, 03 Apr 2021 08:14:54: 15000000 INFO @ Sat, 03 Apr 2021 08:14:57: 10000000 INFO @ Sat, 03 Apr 2021 08:15:00: 6000000 INFO @ Sat, 03 Apr 2021 08:15:00: 16000000 INFO @ Sat, 03 Apr 2021 08:15:04: 11000000 INFO @ Sat, 03 Apr 2021 08:15:06: 7000000 INFO @ Sat, 03 Apr 2021 08:15:06: 17000000 INFO @ Sat, 03 Apr 2021 08:15:10: 12000000 INFO @ Sat, 03 Apr 2021 08:15:12: 8000000 INFO @ Sat, 03 Apr 2021 08:15:12: 18000000 INFO @ Sat, 03 Apr 2021 08:15:17: 13000000 INFO @ Sat, 03 Apr 2021 08:15:18: 19000000 INFO @ Sat, 03 Apr 2021 08:15:18: 9000000 INFO @ Sat, 03 Apr 2021 08:15:23: 14000000 INFO @ Sat, 03 Apr 2021 08:15:24: 20000000 INFO @ Sat, 03 Apr 2021 08:15:25: 10000000 INFO @ Sat, 03 Apr 2021 08:15:30: 15000000 INFO @ Sat, 03 Apr 2021 08:15:30: 21000000 INFO @ Sat, 03 Apr 2021 08:15:31: 11000000 INFO @ Sat, 03 Apr 2021 08:15:36: 16000000 INFO @ Sat, 03 Apr 2021 08:15:36: 22000000 INFO @ Sat, 03 Apr 2021 08:15:37: 12000000 INFO @ Sat, 03 Apr 2021 08:15:42: 17000000 INFO @ Sat, 03 Apr 2021 08:15:42: 23000000 INFO @ Sat, 03 Apr 2021 08:15:43: 13000000 INFO @ Sat, 03 Apr 2021 08:15:48: 18000000 INFO @ Sat, 03 Apr 2021 08:15:48: 24000000 INFO @ Sat, 03 Apr 2021 08:15:49: 14000000 INFO @ Sat, 03 Apr 2021 08:15:54: 19000000 INFO @ Sat, 03 Apr 2021 08:15:54: 25000000 INFO @ Sat, 03 Apr 2021 08:15:56: 15000000 INFO @ Sat, 03 Apr 2021 08:16:00: 20000000 INFO @ Sat, 03 Apr 2021 08:16:01: 26000000 INFO @ Sat, 03 Apr 2021 08:16:02: 16000000 INFO @ Sat, 03 Apr 2021 08:16:06: 21000000 INFO @ Sat, 03 Apr 2021 08:16:07: 27000000 INFO @ Sat, 03 Apr 2021 08:16:08: 17000000 INFO @ Sat, 03 Apr 2021 08:16:12: 22000000 INFO @ Sat, 03 Apr 2021 08:16:13: 28000000 INFO @ Sat, 03 Apr 2021 08:16:14: 18000000 INFO @ Sat, 03 Apr 2021 08:16:18: 23000000 INFO @ Sat, 03 Apr 2021 08:16:19: 29000000 INFO @ Sat, 03 Apr 2021 08:16:20: 19000000 INFO @ Sat, 03 Apr 2021 08:16:25: 24000000 INFO @ Sat, 03 Apr 2021 08:16:25: 30000000 INFO @ Sat, 03 Apr 2021 08:16:25: 20000000 INFO @ Sat, 03 Apr 2021 08:16:31: 25000000 INFO @ Sat, 03 Apr 2021 08:16:31: 21000000 INFO @ Sat, 03 Apr 2021 08:16:32: 31000000 INFO @ Sat, 03 Apr 2021 08:16:37: 26000000 INFO @ Sat, 03 Apr 2021 08:16:37: 22000000 INFO @ Sat, 03 Apr 2021 08:16:38: 32000000 INFO @ Sat, 03 Apr 2021 08:16:43: 27000000 INFO @ Sat, 03 Apr 2021 08:16:43: 23000000 INFO @ Sat, 03 Apr 2021 08:16:44: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:16:49: 24000000 INFO @ Sat, 03 Apr 2021 08:16:50: 28000000 INFO @ Sat, 03 Apr 2021 08:16:50: 34000000 INFO @ Sat, 03 Apr 2021 08:16:55: 25000000 INFO @ Sat, 03 Apr 2021 08:16:56: 29000000 INFO @ Sat, 03 Apr 2021 08:16:56: 35000000 INFO @ Sat, 03 Apr 2021 08:17:02: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:17:02: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:17:02: #1 total tags in treatment: 13730564 INFO @ Sat, 03 Apr 2021 08:17:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:17:02: #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 08:17:02: 26000000 INFO @ Sat, 03 Apr 2021 08:17:02: #1 tags after filtering in treatment: 10100855 INFO @ Sat, 03 Apr 2021 08:17:02: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 08:17:02: #1 finished! INFO @ Sat, 03 Apr 2021 08:17:02: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:17:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:17:02: 30000000 INFO @ Sat, 03 Apr 2021 08:17:03: #2 number of paired peaks: 367 WARNING @ Sat, 03 Apr 2021 08:17:03: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Sat, 03 Apr 2021 08:17:03: start model_add_line... INFO @ Sat, 03 Apr 2021 08:17:03: start X-correlation... INFO @ Sat, 03 Apr 2021 08:17:03: end of X-cor INFO @ Sat, 03 Apr 2021 08:17:03: #2 finished! INFO @ Sat, 03 Apr 2021 08:17:03: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 08:17:03: #2 alternative fragment length(s) may be 4,123,134 bps INFO @ Sat, 03 Apr 2021 08:17:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.05_model.r WARNING @ Sat, 03 Apr 2021 08:17:03: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:17:03: #2 You may need to consider one of the other alternative d(s): 4,123,134 WARNING @ Sat, 03 Apr 2021 08:17:03: #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 08:17:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:17:08: 27000000 INFO @ Sat, 03 Apr 2021 08:17:09: 31000000 INFO @ Sat, 03 Apr 2021 08:17:14: 28000000 INFO @ Sat, 03 Apr 2021 08:17:15: 32000000 INFO @ Sat, 03 Apr 2021 08:17:20: 29000000 INFO @ Sat, 03 Apr 2021 08:17:22: 33000000 INFO @ Sat, 03 Apr 2021 08:17:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:17:27: 30000000 INFO @ Sat, 03 Apr 2021 08:17:28: 34000000 INFO @ Sat, 03 Apr 2021 08:17:33: 31000000 INFO @ Sat, 03 Apr 2021 08:17:34: 35000000 INFO @ Sat, 03 Apr 2021 08:17:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:17:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:17:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.05_summits.bed INFO @ Sat, 03 Apr 2021 08:17:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (490 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:17:39: 32000000 INFO @ Sat, 03 Apr 2021 08:17:40: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:17:40: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:17:40: #1 total tags in treatment: 13730564 INFO @ Sat, 03 Apr 2021 08:17:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:17:40: #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 08:17:40: #1 tags after filtering in treatment: 10100855 INFO @ Sat, 03 Apr 2021 08:17:40: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 08:17:40: #1 finished! INFO @ Sat, 03 Apr 2021 08:17:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:17:41: #2 number of paired peaks: 367 WARNING @ Sat, 03 Apr 2021 08:17:41: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Sat, 03 Apr 2021 08:17:41: start model_add_line... INFO @ Sat, 03 Apr 2021 08:17:41: start X-correlation... INFO @ Sat, 03 Apr 2021 08:17:41: end of X-cor INFO @ Sat, 03 Apr 2021 08:17:41: #2 finished! INFO @ Sat, 03 Apr 2021 08:17:41: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 08:17:41: #2 alternative fragment length(s) may be 4,123,134 bps INFO @ Sat, 03 Apr 2021 08:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.10_model.r WARNING @ Sat, 03 Apr 2021 08:17:41: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:17:41: #2 You may need to consider one of the other alternative d(s): 4,123,134 WARNING @ Sat, 03 Apr 2021 08:17:41: #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 08:17:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:17:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:17:45: 33000000 INFO @ Sat, 03 Apr 2021 08:17:51: 34000000 INFO @ Sat, 03 Apr 2021 08:17:56: 35000000 INFO @ Sat, 03 Apr 2021 08:18:01: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:18:01: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:18:01: #1 total tags in treatment: 13730564 INFO @ Sat, 03 Apr 2021 08:18:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:18:01: #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 08:18:02: #1 tags after filtering in treatment: 10100855 INFO @ Sat, 03 Apr 2021 08:18:02: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 08:18:02: #1 finished! INFO @ Sat, 03 Apr 2021 08:18:02: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:18:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:18:02: #2 number of paired peaks: 367 WARNING @ Sat, 03 Apr 2021 08:18:02: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Sat, 03 Apr 2021 08:18:02: start model_add_line... INFO @ Sat, 03 Apr 2021 08:18:03: start X-correlation... INFO @ Sat, 03 Apr 2021 08:18:03: end of X-cor INFO @ Sat, 03 Apr 2021 08:18:03: #2 finished! INFO @ Sat, 03 Apr 2021 08:18:03: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 08:18:03: #2 alternative fragment length(s) may be 4,123,134 bps INFO @ Sat, 03 Apr 2021 08:18:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.20_model.r WARNING @ Sat, 03 Apr 2021 08:18:03: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:18:03: #2 You may need to consider one of the other alternative d(s): 4,123,134 WARNING @ Sat, 03 Apr 2021 08:18:03: #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 08:18:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:18:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:18:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:18:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:18:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.10_summits.bed INFO @ Sat, 03 Apr 2021 08:18:16: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (311 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:18:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:18:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:18:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:18:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7687151/SRX7687151.20_summits.bed INFO @ Sat, 03 Apr 2021 08:18:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 2 millis CompletedMACS2peakCalling