Job ID = 14159504 SRX = SRX3180816 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: 00:03:17 15558370 reads; of these: 15558370 (100.00%) were unpaired; of these: 1067295 (6.86%) aligned 0 times 12000492 (77.13%) aligned exactly 1 time 2490583 (16.01%) aligned >1 times 93.14% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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] 2785825 / 14491075 = 0.1922 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 22:19:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.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 22:19:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:19:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:19:23: 1000000 INFO @ Wed, 08 Dec 2021 22:19:29: 2000000 INFO @ Wed, 08 Dec 2021 22:19:35: 3000000 INFO @ Wed, 08 Dec 2021 22:19:41: 4000000 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 22:19:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.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 22:19:47: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:19:47: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:19:47: 5000000 INFO @ Wed, 08 Dec 2021 22:19:52: 1000000 INFO @ Wed, 08 Dec 2021 22:19:53: 6000000 INFO @ Wed, 08 Dec 2021 22:19:58: 2000000 INFO @ Wed, 08 Dec 2021 22:19:59: 7000000 INFO @ Wed, 08 Dec 2021 22:20:03: 3000000 INFO @ Wed, 08 Dec 2021 22:20:05: 8000000 INFO @ Wed, 08 Dec 2021 22:20:09: 4000000 INFO @ Wed, 08 Dec 2021 22:20:12: 9000000 INFO @ Wed, 08 Dec 2021 22:20:14: 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 @ Wed, 08 Dec 2021 22:20:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.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 22:20:17: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:20:17: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:20:18: 10000000 INFO @ Wed, 08 Dec 2021 22:20:20: 6000000 INFO @ Wed, 08 Dec 2021 22:20:23: 1000000 INFO @ Wed, 08 Dec 2021 22:20:24: 11000000 INFO @ Wed, 08 Dec 2021 22:20:25: 7000000 INFO @ Wed, 08 Dec 2021 22:20:28: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:20:28: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:20:28: #1 total tags in treatment: 11705250 INFO @ Wed, 08 Dec 2021 22:20:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:20:28: #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 22:20:28: #1 tags after filtering in treatment: 11705250 INFO @ Wed, 08 Dec 2021 22:20:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:20:28: #1 finished! INFO @ Wed, 08 Dec 2021 22:20:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:20:29: 2000000 INFO @ Wed, 08 Dec 2021 22:20:29: #2 number of paired peaks: 348 WARNING @ Wed, 08 Dec 2021 22:20:29: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Wed, 08 Dec 2021 22:20:29: start model_add_line... INFO @ Wed, 08 Dec 2021 22:20:29: start X-correlation... INFO @ Wed, 08 Dec 2021 22:20:29: end of X-cor INFO @ Wed, 08 Dec 2021 22:20:29: #2 finished! INFO @ Wed, 08 Dec 2021 22:20:29: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 22:20:29: #2 alternative fragment length(s) may be 2,50 bps INFO @ Wed, 08 Dec 2021 22:20:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.05_model.r WARNING @ Wed, 08 Dec 2021 22:20:29: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:20:29: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Wed, 08 Dec 2021 22:20:29: #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 22:20:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:20:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:20:31: 8000000 INFO @ Wed, 08 Dec 2021 22:20:34: 3000000 INFO @ Wed, 08 Dec 2021 22:20:36: 9000000 INFO @ Wed, 08 Dec 2021 22:20:39: 4000000 INFO @ Wed, 08 Dec 2021 22:20:41: 10000000 INFO @ Wed, 08 Dec 2021 22:20:45: 5000000 INFO @ Wed, 08 Dec 2021 22:20:47: 11000000 INFO @ Wed, 08 Dec 2021 22:20:50: 6000000 INFO @ Wed, 08 Dec 2021 22:20:51: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:20:51: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:20:51: #1 total tags in treatment: 11705250 INFO @ Wed, 08 Dec 2021 22:20:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:20:51: #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 22:20:51: #1 tags after filtering in treatment: 11705250 INFO @ Wed, 08 Dec 2021 22:20:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:20:51: #1 finished! INFO @ Wed, 08 Dec 2021 22:20:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:20:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:20:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:20:52: #2 number of paired peaks: 348 WARNING @ Wed, 08 Dec 2021 22:20:52: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Wed, 08 Dec 2021 22:20:52: start model_add_line... INFO @ Wed, 08 Dec 2021 22:20:52: start X-correlation... INFO @ Wed, 08 Dec 2021 22:20:52: end of X-cor INFO @ Wed, 08 Dec 2021 22:20:52: #2 finished! INFO @ Wed, 08 Dec 2021 22:20:52: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 22:20:52: #2 alternative fragment length(s) may be 2,50 bps INFO @ Wed, 08 Dec 2021 22:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.10_model.r WARNING @ Wed, 08 Dec 2021 22:20:52: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:20:52: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Wed, 08 Dec 2021 22:20:52: #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 22:20:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:20:55: 7000000 INFO @ Wed, 08 Dec 2021 22:21:00: 8000000 INFO @ Wed, 08 Dec 2021 22:21:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:21:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:21:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.05_summits.bed INFO @ Wed, 08 Dec 2021 22:21:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (669 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:21:05: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:21:10: 10000000 INFO @ Wed, 08 Dec 2021 22:21:13: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:21:15: 11000000 INFO @ Wed, 08 Dec 2021 22:21:19: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 22:21:19: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 22:21:19: #1 total tags in treatment: 11705250 INFO @ Wed, 08 Dec 2021 22:21:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:21:19: #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 22:21:19: #1 tags after filtering in treatment: 11705250 INFO @ Wed, 08 Dec 2021 22:21:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:21:19: #1 finished! INFO @ Wed, 08 Dec 2021 22:21:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:21:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:21:20: #2 number of paired peaks: 348 WARNING @ Wed, 08 Dec 2021 22:21:20: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Wed, 08 Dec 2021 22:21:20: start model_add_line... INFO @ Wed, 08 Dec 2021 22:21:20: start X-correlation... INFO @ Wed, 08 Dec 2021 22:21:20: end of X-cor INFO @ Wed, 08 Dec 2021 22:21:20: #2 finished! INFO @ Wed, 08 Dec 2021 22:21:20: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 22:21:20: #2 alternative fragment length(s) may be 2,50 bps INFO @ Wed, 08 Dec 2021 22:21:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.20_model.r WARNING @ Wed, 08 Dec 2021 22:21:20: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:21:20: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Wed, 08 Dec 2021 22:21:20: #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 22:21:20: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:21:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:21:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:21:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:21:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.10_summits.bed INFO @ Wed, 08 Dec 2021 22:21:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:21:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:21:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:21:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:21:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3180816/SRX3180816.20_summits.bed INFO @ Wed, 08 Dec 2021 22:21:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (201 records, 4 fields): 1 millis CompletedMACS2peakCalling