Job ID = 14159440 SRX = SRX9120621 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: 00:05:10 25118456 reads; of these: 25118456 (100.00%) were unpaired; of these: 808180 (3.22%) aligned 0 times 20322025 (80.90%) aligned exactly 1 time 3988251 (15.88%) aligned >1 times 96.78% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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_rmdupse_core] 3713742 / 24310276 = 0.1528 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 21:59:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.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 21:59:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:59:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:59:27: 1000000 INFO @ Wed, 08 Dec 2021 21:59:32: 2000000 INFO @ Wed, 08 Dec 2021 21:59:38: 3000000 INFO @ Wed, 08 Dec 2021 21:59:43: 4000000 INFO @ Wed, 08 Dec 2021 21:59:48: 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 @ Wed, 08 Dec 2021 21:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.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 @ Wed, 08 Dec 2021 21:59:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:59:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:59:54: 6000000 INFO @ Wed, 08 Dec 2021 21:59:58: 1000000 INFO @ Wed, 08 Dec 2021 22:00:00: 7000000 INFO @ Wed, 08 Dec 2021 22:00:06: 2000000 INFO @ Wed, 08 Dec 2021 22:00:07: 8000000 INFO @ Wed, 08 Dec 2021 22:00:13: 3000000 INFO @ Wed, 08 Dec 2021 22:00:13: 9000000 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 @ Wed, 08 Dec 2021 22:00:20: 10000000 INFO @ Wed, 08 Dec 2021 22:00:20: 4000000 INFO @ Wed, 08 Dec 2021 22:00:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.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 @ Wed, 08 Dec 2021 22:00:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:00:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:00:27: 11000000 INFO @ Wed, 08 Dec 2021 22:00:27: 5000000 INFO @ Wed, 08 Dec 2021 22:00:28: 1000000 INFO @ Wed, 08 Dec 2021 22:00:33: 12000000 INFO @ Wed, 08 Dec 2021 22:00:34: 2000000 INFO @ Wed, 08 Dec 2021 22:00:34: 6000000 INFO @ Wed, 08 Dec 2021 22:00:40: 13000000 INFO @ Wed, 08 Dec 2021 22:00:41: 3000000 INFO @ Wed, 08 Dec 2021 22:00:42: 7000000 INFO @ Wed, 08 Dec 2021 22:00:47: 14000000 INFO @ Wed, 08 Dec 2021 22:00:48: 4000000 INFO @ Wed, 08 Dec 2021 22:00:49: 8000000 INFO @ Wed, 08 Dec 2021 22:00:54: 15000000 INFO @ Wed, 08 Dec 2021 22:00:55: 5000000 INFO @ Wed, 08 Dec 2021 22:00:56: 9000000 INFO @ Wed, 08 Dec 2021 22:01:01: 16000000 INFO @ Wed, 08 Dec 2021 22:01:01: 6000000 INFO @ Wed, 08 Dec 2021 22:01:03: 10000000 INFO @ Wed, 08 Dec 2021 22:01:07: 17000000 INFO @ Wed, 08 Dec 2021 22:01:08: 7000000 INFO @ Wed, 08 Dec 2021 22:01:10: 11000000 INFO @ Wed, 08 Dec 2021 22:01:14: 18000000 INFO @ Wed, 08 Dec 2021 22:01:15: 8000000 INFO @ Wed, 08 Dec 2021 22:01:18: 12000000 INFO @ Wed, 08 Dec 2021 22:01:21: 19000000 INFO @ Wed, 08 Dec 2021 22:01:22: 9000000 INFO @ Wed, 08 Dec 2021 22:01:25: 13000000 INFO @ Wed, 08 Dec 2021 22:01:28: 20000000 INFO @ Wed, 08 Dec 2021 22:01:28: 10000000 INFO @ Wed, 08 Dec 2021 22:01:32: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:01:32: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:01:32: #1 total tags in treatment: 20596534 INFO @ Wed, 08 Dec 2021 22:01:32: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:01:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:01:32: #1 tags after filtering in treatment: 20596534 INFO @ Wed, 08 Dec 2021 22:01:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:01:32: #1 finished! INFO @ Wed, 08 Dec 2021 22:01:32: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:01:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:01:32: 14000000 INFO @ Wed, 08 Dec 2021 22:01:33: #2 number of paired peaks: 176 WARNING @ Wed, 08 Dec 2021 22:01:33: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Wed, 08 Dec 2021 22:01:33: start model_add_line... INFO @ Wed, 08 Dec 2021 22:01:33: start X-correlation... INFO @ Wed, 08 Dec 2021 22:01:33: end of X-cor INFO @ Wed, 08 Dec 2021 22:01:33: #2 finished! INFO @ Wed, 08 Dec 2021 22:01:33: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:01:33: #2 alternative fragment length(s) may be 1,49,512,533,555,581 bps INFO @ Wed, 08 Dec 2021 22:01:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.05_model.r WARNING @ Wed, 08 Dec 2021 22:01:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:01:33: #2 You may need to consider one of the other alternative d(s): 1,49,512,533,555,581 WARNING @ Wed, 08 Dec 2021 22:01:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:01:33: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:01:35: 11000000 INFO @ Wed, 08 Dec 2021 22:01:39: 15000000 INFO @ Wed, 08 Dec 2021 22:01:41: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:01:46: 16000000 INFO @ Wed, 08 Dec 2021 22:01:48: 13000000 INFO @ Wed, 08 Dec 2021 22:01:53: 17000000 INFO @ Wed, 08 Dec 2021 22:01:54: 14000000 INFO @ Wed, 08 Dec 2021 22:02:01: 18000000 INFO @ Wed, 08 Dec 2021 22:02:01: 15000000 INFO @ Wed, 08 Dec 2021 22:02:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:02:07: 16000000 INFO @ Wed, 08 Dec 2021 22:02:08: 19000000 INFO @ Wed, 08 Dec 2021 22:02:14: 17000000 INFO @ Wed, 08 Dec 2021 22:02:15: 20000000 INFO @ Wed, 08 Dec 2021 22:02:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:02:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:02:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.05_summits.bed INFO @ Wed, 08 Dec 2021 22:02:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:02:19: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:02:19: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:02:19: #1 total tags in treatment: 20596534 INFO @ Wed, 08 Dec 2021 22:02:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:02:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:02:19: #1 tags after filtering in treatment: 20596534 INFO @ Wed, 08 Dec 2021 22:02:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:02:19: #1 finished! INFO @ Wed, 08 Dec 2021 22:02:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:02:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:02:20: 18000000 INFO @ Wed, 08 Dec 2021 22:02:21: #2 number of paired peaks: 176 WARNING @ Wed, 08 Dec 2021 22:02:21: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Wed, 08 Dec 2021 22:02:21: start model_add_line... INFO @ Wed, 08 Dec 2021 22:02:21: start X-correlation... INFO @ Wed, 08 Dec 2021 22:02:21: end of X-cor INFO @ Wed, 08 Dec 2021 22:02:21: #2 finished! INFO @ Wed, 08 Dec 2021 22:02:21: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:02:21: #2 alternative fragment length(s) may be 1,49,512,533,555,581 bps INFO @ Wed, 08 Dec 2021 22:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.10_model.r WARNING @ Wed, 08 Dec 2021 22:02:21: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:02:21: #2 You may need to consider one of the other alternative d(s): 1,49,512,533,555,581 WARNING @ Wed, 08 Dec 2021 22:02:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:02:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:02:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:02:26: 19000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:02:32: 20000000 INFO @ Wed, 08 Dec 2021 22:02:35: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:02:35: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:02:35: #1 total tags in treatment: 20596534 INFO @ Wed, 08 Dec 2021 22:02:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:02:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:02:36: #1 tags after filtering in treatment: 20596534 INFO @ Wed, 08 Dec 2021 22:02:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:02:36: #1 finished! INFO @ Wed, 08 Dec 2021 22:02:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:02:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:02:37: #2 number of paired peaks: 176 WARNING @ Wed, 08 Dec 2021 22:02:37: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Wed, 08 Dec 2021 22:02:37: start model_add_line... INFO @ Wed, 08 Dec 2021 22:02:37: start X-correlation... INFO @ Wed, 08 Dec 2021 22:02:37: end of X-cor INFO @ Wed, 08 Dec 2021 22:02:37: #2 finished! INFO @ Wed, 08 Dec 2021 22:02:37: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:02:37: #2 alternative fragment length(s) may be 1,49,512,533,555,581 bps INFO @ Wed, 08 Dec 2021 22:02:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.20_model.r WARNING @ Wed, 08 Dec 2021 22:02:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:02:37: #2 You may need to consider one of the other alternative d(s): 1,49,512,533,555,581 WARNING @ Wed, 08 Dec 2021 22:02:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:02:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:02:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:02:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:03:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:03:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:03:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.10_summits.bed INFO @ Wed, 08 Dec 2021 22:03:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:03:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:03:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:03:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:03:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120621/SRX9120621.20_summits.bed INFO @ Wed, 08 Dec 2021 22:03:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling