Job ID = 12265426 SRX = SRX4082401 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: 00:25:16 216855011 reads; of these: 216855011 (100.00%) were unpaired; of these: 152784582 (70.45%) aligned 0 times 56466457 (26.04%) aligned exactly 1 time 7603972 (3.51%) aligned >1 times 29.55% overall alignment rate Time searching: 00:25:16 Overall time: 00:25:16 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_rmdupse_core] 43015293 / 64070429 = 0.6714 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 07:35:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.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 07:35:56: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:35:56: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:36:01: 1000000 INFO @ Sat, 03 Apr 2021 07:36:06: 2000000 INFO @ Sat, 03 Apr 2021 07:36:11: 3000000 INFO @ Sat, 03 Apr 2021 07:36:16: 4000000 INFO @ Sat, 03 Apr 2021 07:36:21: 5000000 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 07:36:26: 6000000 INFO @ Sat, 03 Apr 2021 07:36:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.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 07:36:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:36:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:36:31: 7000000 INFO @ Sat, 03 Apr 2021 07:36:34: 1000000 INFO @ Sat, 03 Apr 2021 07:36:35: 8000000 INFO @ Sat, 03 Apr 2021 07:36:39: 2000000 INFO @ Sat, 03 Apr 2021 07:36:40: 9000000 INFO @ Sat, 03 Apr 2021 07:36:44: 3000000 INFO @ Sat, 03 Apr 2021 07:36:45: 10000000 INFO @ Sat, 03 Apr 2021 07:36:49: 4000000 INFO @ Sat, 03 Apr 2021 07:36:50: 11000000 INFO @ Sat, 03 Apr 2021 07:36:54: 5000000 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 07:36:55: 12000000 INFO @ Sat, 03 Apr 2021 07:36:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.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 07:36:56: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:36:56: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:36:59: 6000000 INFO @ Sat, 03 Apr 2021 07:37:00: 13000000 INFO @ Sat, 03 Apr 2021 07:37:01: 1000000 INFO @ Sat, 03 Apr 2021 07:37:04: 7000000 INFO @ Sat, 03 Apr 2021 07:37:05: 14000000 INFO @ Sat, 03 Apr 2021 07:37:06: 2000000 INFO @ Sat, 03 Apr 2021 07:37:09: 8000000 INFO @ Sat, 03 Apr 2021 07:37:10: 15000000 INFO @ Sat, 03 Apr 2021 07:37:12: 3000000 INFO @ Sat, 03 Apr 2021 07:37:14: 9000000 INFO @ Sat, 03 Apr 2021 07:37:15: 16000000 INFO @ Sat, 03 Apr 2021 07:37:17: 4000000 INFO @ Sat, 03 Apr 2021 07:37:19: 10000000 INFO @ Sat, 03 Apr 2021 07:37:20: 17000000 INFO @ Sat, 03 Apr 2021 07:37:22: 5000000 INFO @ Sat, 03 Apr 2021 07:37:24: 11000000 INFO @ Sat, 03 Apr 2021 07:37:25: 18000000 INFO @ Sat, 03 Apr 2021 07:37:27: 6000000 INFO @ Sat, 03 Apr 2021 07:37:29: 12000000 INFO @ Sat, 03 Apr 2021 07:37:30: 19000000 INFO @ Sat, 03 Apr 2021 07:37:32: 7000000 INFO @ Sat, 03 Apr 2021 07:37:34: 13000000 INFO @ Sat, 03 Apr 2021 07:37:35: 20000000 INFO @ Sat, 03 Apr 2021 07:37:37: 8000000 INFO @ Sat, 03 Apr 2021 07:37:39: 14000000 INFO @ Sat, 03 Apr 2021 07:37:40: 21000000 INFO @ Sat, 03 Apr 2021 07:37:40: #1 tag size is determined as 47 bps INFO @ Sat, 03 Apr 2021 07:37:40: #1 tag size = 47 INFO @ Sat, 03 Apr 2021 07:37:40: #1 total tags in treatment: 21055136 INFO @ Sat, 03 Apr 2021 07:37:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:37:40: #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 07:37:41: #1 tags after filtering in treatment: 21055136 INFO @ Sat, 03 Apr 2021 07:37:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:37:41: #1 finished! INFO @ Sat, 03 Apr 2021 07:37:41: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:37:42: 9000000 INFO @ Sat, 03 Apr 2021 07:37:42: #2 number of paired peaks: 253 WARNING @ Sat, 03 Apr 2021 07:37:42: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sat, 03 Apr 2021 07:37:42: start model_add_line... INFO @ Sat, 03 Apr 2021 07:37:42: start X-correlation... INFO @ Sat, 03 Apr 2021 07:37:42: end of X-cor INFO @ Sat, 03 Apr 2021 07:37:42: #2 finished! INFO @ Sat, 03 Apr 2021 07:37:42: #2 predicted fragment length is 60 bps INFO @ Sat, 03 Apr 2021 07:37:42: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sat, 03 Apr 2021 07:37:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.05_model.r WARNING @ Sat, 03 Apr 2021 07:37:42: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:37:42: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sat, 03 Apr 2021 07:37:42: #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 07:37:42: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:37:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:37:44: 15000000 INFO @ Sat, 03 Apr 2021 07:37:47: 10000000 INFO @ Sat, 03 Apr 2021 07:37:49: 16000000 INFO @ Sat, 03 Apr 2021 07:37:52: 11000000 INFO @ Sat, 03 Apr 2021 07:37:54: 17000000 INFO @ Sat, 03 Apr 2021 07:37:57: 12000000 INFO @ Sat, 03 Apr 2021 07:37:59: 18000000 INFO @ Sat, 03 Apr 2021 07:38:02: 13000000 INFO @ Sat, 03 Apr 2021 07:38:04: 19000000 INFO @ Sat, 03 Apr 2021 07:38:07: 14000000 INFO @ Sat, 03 Apr 2021 07:38:09: 20000000 INFO @ Sat, 03 Apr 2021 07:38:12: 15000000 INFO @ Sat, 03 Apr 2021 07:38:14: 21000000 INFO @ Sat, 03 Apr 2021 07:38:14: #1 tag size is determined as 47 bps INFO @ Sat, 03 Apr 2021 07:38:14: #1 tag size = 47 INFO @ Sat, 03 Apr 2021 07:38:14: #1 total tags in treatment: 21055136 INFO @ Sat, 03 Apr 2021 07:38:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:38:14: #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 07:38:14: #1 tags after filtering in treatment: 21055136 INFO @ Sat, 03 Apr 2021 07:38:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:38:14: #1 finished! INFO @ Sat, 03 Apr 2021 07:38:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:38:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:38:16: #2 number of paired peaks: 253 WARNING @ Sat, 03 Apr 2021 07:38:16: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sat, 03 Apr 2021 07:38:16: start model_add_line... INFO @ Sat, 03 Apr 2021 07:38:16: start X-correlation... INFO @ Sat, 03 Apr 2021 07:38:16: end of X-cor INFO @ Sat, 03 Apr 2021 07:38:16: #2 finished! INFO @ Sat, 03 Apr 2021 07:38:16: #2 predicted fragment length is 60 bps INFO @ Sat, 03 Apr 2021 07:38:16: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sat, 03 Apr 2021 07:38:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.10_model.r WARNING @ Sat, 03 Apr 2021 07:38:16: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:38:16: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sat, 03 Apr 2021 07:38:16: #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 07:38:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:38:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:38:16: 16000000 INFO @ Sat, 03 Apr 2021 07:38:21: 17000000 INFO @ Sat, 03 Apr 2021 07:38:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:38:26: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:38:31: 19000000 INFO @ Sat, 03 Apr 2021 07:38:36: 20000000 INFO @ Sat, 03 Apr 2021 07:38:42: 21000000 INFO @ Sat, 03 Apr 2021 07:38:42: #1 tag size is determined as 47 bps INFO @ Sat, 03 Apr 2021 07:38:42: #1 tag size = 47 INFO @ Sat, 03 Apr 2021 07:38:42: #1 total tags in treatment: 21055136 INFO @ Sat, 03 Apr 2021 07:38:42: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:38:42: #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 07:38:42: #1 tags after filtering in treatment: 21055136 INFO @ Sat, 03 Apr 2021 07:38:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:38:42: #1 finished! INFO @ Sat, 03 Apr 2021 07:38:42: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:38:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:38:44: #2 number of paired peaks: 253 WARNING @ Sat, 03 Apr 2021 07:38:44: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sat, 03 Apr 2021 07:38:44: start model_add_line... INFO @ Sat, 03 Apr 2021 07:38:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:38:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:38:44: start X-correlation... INFO @ Sat, 03 Apr 2021 07:38:44: end of X-cor INFO @ Sat, 03 Apr 2021 07:38:44: #2 finished! INFO @ Sat, 03 Apr 2021 07:38:44: #2 predicted fragment length is 60 bps INFO @ Sat, 03 Apr 2021 07:38:44: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sat, 03 Apr 2021 07:38:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.20_model.r WARNING @ Sat, 03 Apr 2021 07:38:44: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:38:44: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sat, 03 Apr 2021 07:38:44: #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 07:38:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:38:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.05_summits.bed INFO @ Sat, 03 Apr 2021 07:38:44: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (18098 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:38:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:39:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:39:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:39:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.10_summits.bed INFO @ Sat, 03 Apr 2021 07:39:18: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10859 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:39:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:39:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:39:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:39:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082401/SRX4082401.20_summits.bed INFO @ Sat, 03 Apr 2021 07:39:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3988 records, 4 fields): 5 millis CompletedMACS2peakCalling