Job ID = 14158039 SRX = SRX10569199 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: 00:07:53 28187416 reads; of these: 28187416 (100.00%) were unpaired; of these: 9267447 (32.88%) aligned 0 times 15761052 (55.92%) aligned exactly 1 time 3158917 (11.21%) aligned >1 times 67.12% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 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 8 files... [bam_rmdupse_core] 2787672 / 18919969 = 0.1473 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 14:13:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.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 14:13:07: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:13:07: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:13:14: 1000000 INFO @ Wed, 08 Dec 2021 14:13:21: 2000000 INFO @ Wed, 08 Dec 2021 14:13:28: 3000000 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 14:13:35: 4000000 INFO @ Wed, 08 Dec 2021 14:13:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.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 14:13:37: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:13:37: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:13:43: 5000000 INFO @ Wed, 08 Dec 2021 14:13:43: 1000000 INFO @ Wed, 08 Dec 2021 14:13:50: 2000000 INFO @ Wed, 08 Dec 2021 14:13:50: 6000000 INFO @ Wed, 08 Dec 2021 14:13:57: 3000000 INFO @ Wed, 08 Dec 2021 14:13:58: 7000000 INFO @ Wed, 08 Dec 2021 14:14:03: 4000000 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 14:14:06: 8000000 INFO @ Wed, 08 Dec 2021 14:14:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.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 14:14:07: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:14:07: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:14:10: 5000000 INFO @ Wed, 08 Dec 2021 14:14:13: 9000000 INFO @ Wed, 08 Dec 2021 14:14:14: 1000000 INFO @ Wed, 08 Dec 2021 14:14:17: 6000000 INFO @ Wed, 08 Dec 2021 14:14:21: 10000000 INFO @ Wed, 08 Dec 2021 14:14:21: 2000000 INFO @ Wed, 08 Dec 2021 14:14:24: 7000000 INFO @ Wed, 08 Dec 2021 14:14:28: 3000000 INFO @ Wed, 08 Dec 2021 14:14:29: 11000000 INFO @ Wed, 08 Dec 2021 14:14:31: 8000000 INFO @ Wed, 08 Dec 2021 14:14:35: 4000000 INFO @ Wed, 08 Dec 2021 14:14:36: 12000000 INFO @ Wed, 08 Dec 2021 14:14:38: 9000000 INFO @ Wed, 08 Dec 2021 14:14:43: 5000000 INFO @ Wed, 08 Dec 2021 14:14:44: 13000000 INFO @ Wed, 08 Dec 2021 14:14:45: 10000000 INFO @ Wed, 08 Dec 2021 14:14:51: 6000000 INFO @ Wed, 08 Dec 2021 14:14:51: 14000000 INFO @ Wed, 08 Dec 2021 14:14:52: 11000000 INFO @ Wed, 08 Dec 2021 14:14:58: 12000000 INFO @ Wed, 08 Dec 2021 14:14:58: 7000000 INFO @ Wed, 08 Dec 2021 14:14:58: 15000000 INFO @ Wed, 08 Dec 2021 14:15:05: 13000000 INFO @ Wed, 08 Dec 2021 14:15:06: 8000000 INFO @ Wed, 08 Dec 2021 14:15:06: 16000000 INFO @ Wed, 08 Dec 2021 14:15:07: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 14:15:07: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 14:15:07: #1 total tags in treatment: 16132297 INFO @ Wed, 08 Dec 2021 14:15:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:15:07: #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 14:15:07: #1 tags after filtering in treatment: 16132297 INFO @ Wed, 08 Dec 2021 14:15:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:15:07: #1 finished! INFO @ Wed, 08 Dec 2021 14:15:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:15:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:15:08: #2 number of paired peaks: 196 WARNING @ Wed, 08 Dec 2021 14:15:08: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Wed, 08 Dec 2021 14:15:08: start model_add_line... INFO @ Wed, 08 Dec 2021 14:15:08: start X-correlation... INFO @ Wed, 08 Dec 2021 14:15:08: end of X-cor INFO @ Wed, 08 Dec 2021 14:15:08: #2 finished! INFO @ Wed, 08 Dec 2021 14:15:08: #2 predicted fragment length is 58 bps INFO @ Wed, 08 Dec 2021 14:15:08: #2 alternative fragment length(s) may be 2,58,574 bps INFO @ Wed, 08 Dec 2021 14:15:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.05_model.r WARNING @ Wed, 08 Dec 2021 14:15:08: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:15:08: #2 You may need to consider one of the other alternative d(s): 2,58,574 WARNING @ Wed, 08 Dec 2021 14:15:08: #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 14:15:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:15:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:15:11: 14000000 INFO @ Wed, 08 Dec 2021 14:15:13: 9000000 INFO @ Wed, 08 Dec 2021 14:15:18: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:15:21: 10000000 INFO @ Wed, 08 Dec 2021 14:15:24: 16000000 INFO @ Wed, 08 Dec 2021 14:15:25: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 14:15:25: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 14:15:25: #1 total tags in treatment: 16132297 INFO @ Wed, 08 Dec 2021 14:15:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:15:25: #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 14:15:26: #1 tags after filtering in treatment: 16132297 INFO @ Wed, 08 Dec 2021 14:15:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:15:26: #1 finished! INFO @ Wed, 08 Dec 2021 14:15:26: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:15:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:15:27: #2 number of paired peaks: 196 WARNING @ Wed, 08 Dec 2021 14:15:27: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Wed, 08 Dec 2021 14:15:27: start model_add_line... INFO @ Wed, 08 Dec 2021 14:15:27: start X-correlation... INFO @ Wed, 08 Dec 2021 14:15:27: end of X-cor INFO @ Wed, 08 Dec 2021 14:15:27: #2 finished! INFO @ Wed, 08 Dec 2021 14:15:27: #2 predicted fragment length is 58 bps INFO @ Wed, 08 Dec 2021 14:15:27: #2 alternative fragment length(s) may be 2,58,574 bps INFO @ Wed, 08 Dec 2021 14:15:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.10_model.r WARNING @ Wed, 08 Dec 2021 14:15:27: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:15:27: #2 You may need to consider one of the other alternative d(s): 2,58,574 WARNING @ Wed, 08 Dec 2021 14:15:27: #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 14:15:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:15:28: 11000000 INFO @ Wed, 08 Dec 2021 14:15:35: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:15:35: 12000000 INFO @ Wed, 08 Dec 2021 14:15:42: 13000000 INFO @ Wed, 08 Dec 2021 14:15:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:15:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:15:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.05_summits.bed INFO @ Wed, 08 Dec 2021 14:15:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (500 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:15:49: 14000000 INFO @ Wed, 08 Dec 2021 14:15:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:15:56: 15000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:16:03: 16000000 INFO @ Wed, 08 Dec 2021 14:16:04: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 14:16:04: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 14:16:04: #1 total tags in treatment: 16132297 INFO @ Wed, 08 Dec 2021 14:16:04: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:16:04: #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 14:16:04: #1 tags after filtering in treatment: 16132297 INFO @ Wed, 08 Dec 2021 14:16:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:16:04: #1 finished! INFO @ Wed, 08 Dec 2021 14:16:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:16:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:16:05: #2 number of paired peaks: 196 WARNING @ Wed, 08 Dec 2021 14:16:05: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Wed, 08 Dec 2021 14:16:05: start model_add_line... INFO @ Wed, 08 Dec 2021 14:16:05: start X-correlation... INFO @ Wed, 08 Dec 2021 14:16:05: end of X-cor INFO @ Wed, 08 Dec 2021 14:16:05: #2 finished! INFO @ Wed, 08 Dec 2021 14:16:05: #2 predicted fragment length is 58 bps INFO @ Wed, 08 Dec 2021 14:16:05: #2 alternative fragment length(s) may be 2,58,574 bps INFO @ Wed, 08 Dec 2021 14:16:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.20_model.r WARNING @ Wed, 08 Dec 2021 14:16:05: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:16:05: #2 You may need to consider one of the other alternative d(s): 2,58,574 WARNING @ Wed, 08 Dec 2021 14:16:05: #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 14:16:05: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:16:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:16:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:16:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:16:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.10_summits.bed INFO @ Wed, 08 Dec 2021 14:16:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (329 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:16:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:16:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10569199/SRX10569199.20_summits.bed INFO @ Wed, 08 Dec 2021 14:16:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (130 records, 4 fields): 1 millis CompletedMACS2peakCalling