Job ID = 14160679 SRX = SRX8331160 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE 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: 00:14:31 39676651 reads; of these: 39676651 (100.00%) were unpaired; of these: 165809 (0.42%) aligned 0 times 33489282 (84.41%) aligned exactly 1 time 6021560 (15.18%) aligned >1 times 99.58% overall alignment rate Time searching: 00:14:31 Overall time: 00:14:31 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_rmdupse_core] 15330277 / 39510842 = 0.3880 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 04:07:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.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 04:07:04: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:07:04: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:07:15: 1000000 INFO @ Thu, 09 Dec 2021 04:07:26: 2000000 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 04:07:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.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 04:07:34: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:07:34: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:07:37: 3000000 INFO @ Thu, 09 Dec 2021 04:07:44: 1000000 INFO @ Thu, 09 Dec 2021 04:07:48: 4000000 INFO @ Thu, 09 Dec 2021 04:07:54: 2000000 INFO @ Thu, 09 Dec 2021 04:08:00: 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 04:08:03: 3000000 INFO @ Thu, 09 Dec 2021 04:08:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.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 04:08:04: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:08:04: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:08:11: 6000000 INFO @ Thu, 09 Dec 2021 04:08:13: 4000000 INFO @ Thu, 09 Dec 2021 04:08:18: 1000000 INFO @ Thu, 09 Dec 2021 04:08:22: 5000000 INFO @ Thu, 09 Dec 2021 04:08:23: 7000000 INFO @ Thu, 09 Dec 2021 04:08:32: 2000000 INFO @ Thu, 09 Dec 2021 04:08:32: 6000000 INFO @ Thu, 09 Dec 2021 04:08:35: 8000000 INFO @ Thu, 09 Dec 2021 04:08:41: 7000000 INFO @ Thu, 09 Dec 2021 04:08:45: 3000000 INFO @ Thu, 09 Dec 2021 04:08:46: 9000000 INFO @ Thu, 09 Dec 2021 04:08:51: 8000000 INFO @ Thu, 09 Dec 2021 04:08:57: 10000000 INFO @ Thu, 09 Dec 2021 04:08:59: 4000000 INFO @ Thu, 09 Dec 2021 04:09:01: 9000000 INFO @ Thu, 09 Dec 2021 04:09:09: 11000000 INFO @ Thu, 09 Dec 2021 04:09:10: 10000000 INFO @ Thu, 09 Dec 2021 04:09:12: 5000000 INFO @ Thu, 09 Dec 2021 04:09:20: 11000000 INFO @ Thu, 09 Dec 2021 04:09:20: 12000000 INFO @ Thu, 09 Dec 2021 04:09:26: 6000000 INFO @ Thu, 09 Dec 2021 04:09:30: 12000000 INFO @ Thu, 09 Dec 2021 04:09:32: 13000000 INFO @ Thu, 09 Dec 2021 04:09:40: 7000000 INFO @ Thu, 09 Dec 2021 04:09:40: 13000000 INFO @ Thu, 09 Dec 2021 04:09:43: 14000000 INFO @ Thu, 09 Dec 2021 04:09:50: 14000000 INFO @ Thu, 09 Dec 2021 04:09:54: 8000000 INFO @ Thu, 09 Dec 2021 04:09:54: 15000000 INFO @ Thu, 09 Dec 2021 04:10:01: 15000000 INFO @ Thu, 09 Dec 2021 04:10:06: 16000000 INFO @ Thu, 09 Dec 2021 04:10:08: 9000000 INFO @ Thu, 09 Dec 2021 04:10:13: 16000000 INFO @ Thu, 09 Dec 2021 04:10:17: 17000000 INFO @ Thu, 09 Dec 2021 04:10:23: 10000000 INFO @ Thu, 09 Dec 2021 04:10:24: 17000000 INFO @ Thu, 09 Dec 2021 04:10:29: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:10:35: 18000000 INFO @ Thu, 09 Dec 2021 04:10:37: 11000000 INFO @ Thu, 09 Dec 2021 04:10:40: 19000000 INFO @ Thu, 09 Dec 2021 04:10:47: 19000000 INFO @ Thu, 09 Dec 2021 04:10:51: 12000000 INFO @ Thu, 09 Dec 2021 04:10:52: 20000000 INFO @ Thu, 09 Dec 2021 04:10:58: 20000000 INFO @ Thu, 09 Dec 2021 04:11:04: 21000000 INFO @ Thu, 09 Dec 2021 04:11:06: 13000000 INFO @ Thu, 09 Dec 2021 04:11:08: 21000000 INFO @ Thu, 09 Dec 2021 04:11:14: 22000000 INFO @ Thu, 09 Dec 2021 04:11:18: 22000000 INFO @ Thu, 09 Dec 2021 04:11:20: 14000000 INFO @ Thu, 09 Dec 2021 04:11:25: 23000000 INFO @ Thu, 09 Dec 2021 04:11:27: 23000000 INFO @ Thu, 09 Dec 2021 04:11:33: 15000000 INFO @ Thu, 09 Dec 2021 04:11:36: 24000000 INFO @ Thu, 09 Dec 2021 04:11:37: 24000000 INFO @ Thu, 09 Dec 2021 04:11:38: #1 tag size is determined as 74 bps INFO @ Thu, 09 Dec 2021 04:11:38: #1 tag size = 74 INFO @ Thu, 09 Dec 2021 04:11:38: #1 total tags in treatment: 24180565 INFO @ Thu, 09 Dec 2021 04:11:38: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:11:38: #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 04:11:38: #1 tag size is determined as 74 bps INFO @ Thu, 09 Dec 2021 04:11:38: #1 tag size = 74 INFO @ Thu, 09 Dec 2021 04:11:38: #1 total tags in treatment: 24180565 INFO @ Thu, 09 Dec 2021 04:11:38: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:11:38: #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 04:11:38: #1 tags after filtering in treatment: 24180565 INFO @ Thu, 09 Dec 2021 04:11:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:11:38: #1 finished! INFO @ Thu, 09 Dec 2021 04:11:38: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:11:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:11:39: #1 tags after filtering in treatment: 24180565 INFO @ Thu, 09 Dec 2021 04:11:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:11:39: #1 finished! INFO @ Thu, 09 Dec 2021 04:11:39: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:11:40: #2 number of paired peaks: 135 WARNING @ Thu, 09 Dec 2021 04:11:40: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Thu, 09 Dec 2021 04:11:40: start model_add_line... INFO @ Thu, 09 Dec 2021 04:11:40: start X-correlation... INFO @ Thu, 09 Dec 2021 04:11:40: end of X-cor INFO @ Thu, 09 Dec 2021 04:11:40: #2 finished! INFO @ Thu, 09 Dec 2021 04:11:40: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 04:11:40: #2 alternative fragment length(s) may be 1,33,65,567,589 bps INFO @ Thu, 09 Dec 2021 04:11:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.05_model.r WARNING @ Thu, 09 Dec 2021 04:11:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:11:40: #2 You may need to consider one of the other alternative d(s): 1,33,65,567,589 WARNING @ Thu, 09 Dec 2021 04:11:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:11:40: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:11:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:11:41: #2 number of paired peaks: 135 WARNING @ Thu, 09 Dec 2021 04:11:41: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Thu, 09 Dec 2021 04:11:41: start model_add_line... INFO @ Thu, 09 Dec 2021 04:11:41: start X-correlation... INFO @ Thu, 09 Dec 2021 04:11:41: end of X-cor INFO @ Thu, 09 Dec 2021 04:11:41: #2 finished! INFO @ Thu, 09 Dec 2021 04:11:41: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 04:11:41: #2 alternative fragment length(s) may be 1,33,65,567,589 bps INFO @ Thu, 09 Dec 2021 04:11:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.10_model.r WARNING @ Thu, 09 Dec 2021 04:11:41: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:11:41: #2 You may need to consider one of the other alternative d(s): 1,33,65,567,589 WARNING @ Thu, 09 Dec 2021 04:11:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:11:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:11:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:11:47: 16000000 INFO @ Thu, 09 Dec 2021 04:12:00: 17000000 INFO @ Thu, 09 Dec 2021 04:12:14: 18000000 INFO @ Thu, 09 Dec 2021 04:12:27: 19000000 INFO @ Thu, 09 Dec 2021 04:12:30: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:12:30: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:12:40: 20000000 INFO @ Thu, 09 Dec 2021 04:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.10_summits.bed INFO @ Thu, 09 Dec 2021 04:12:52: Done! INFO @ Thu, 09 Dec 2021 04:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.05_summits.bed INFO @ Thu, 09 Dec 2021 04:12:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:12:53: 21000000 INFO @ Thu, 09 Dec 2021 04:13:06: 22000000 INFO @ Thu, 09 Dec 2021 04:13:19: 23000000 INFO @ Thu, 09 Dec 2021 04:13:33: 24000000 INFO @ Thu, 09 Dec 2021 04:13:35: #1 tag size is determined as 74 bps INFO @ Thu, 09 Dec 2021 04:13:35: #1 tag size = 74 INFO @ Thu, 09 Dec 2021 04:13:35: #1 total tags in treatment: 24180565 INFO @ Thu, 09 Dec 2021 04:13:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:13:35: #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 04:13:35: #1 tags after filtering in treatment: 24180565 INFO @ Thu, 09 Dec 2021 04:13:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:13:35: #1 finished! INFO @ Thu, 09 Dec 2021 04:13:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:13:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:13:37: #2 number of paired peaks: 135 WARNING @ Thu, 09 Dec 2021 04:13:37: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Thu, 09 Dec 2021 04:13:37: start model_add_line... INFO @ Thu, 09 Dec 2021 04:13:37: start X-correlation... INFO @ Thu, 09 Dec 2021 04:13:37: end of X-cor INFO @ Thu, 09 Dec 2021 04:13:37: #2 finished! INFO @ Thu, 09 Dec 2021 04:13:37: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 04:13:37: #2 alternative fragment length(s) may be 1,33,65,567,589 bps INFO @ Thu, 09 Dec 2021 04:13:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.20_model.r WARNING @ Thu, 09 Dec 2021 04:13:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:13:37: #2 You may need to consider one of the other alternative d(s): 1,33,65,567,589 WARNING @ Thu, 09 Dec 2021 04:13:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:13:37: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:13:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:14:27: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:14:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:14:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:14:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331160/SRX8331160.20_summits.bed INFO @ Thu, 09 Dec 2021 04:14:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling