Job ID = 6626606 SRX = SRX7630546 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: 00:06:39 41859759 reads; of these: 41859759 (100.00%) were unpaired; of these: 15979950 (38.17%) aligned 0 times 21433711 (51.20%) aligned exactly 1 time 4446098 (10.62%) aligned >1 times 61.83% overall alignment rate Time searching: 00:06:39 Overall time: 00:06:39 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] 8236001 / 25879809 = 0.3182 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:01:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.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 @ Tue, 14 Jul 2020 08:01:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:01:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:01:24: 1000000 INFO @ Tue, 14 Jul 2020 08:01:29: 2000000 INFO @ Tue, 14 Jul 2020 08:01:33: 3000000 INFO @ Tue, 14 Jul 2020 08:01:38: 4000000 INFO @ Tue, 14 Jul 2020 08:01:42: 5000000 INFO @ Tue, 14 Jul 2020 08:01:47: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:01:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.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 @ Tue, 14 Jul 2020 08:01:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:01:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:01:52: 7000000 INFO @ Tue, 14 Jul 2020 08:01:55: 1000000 INFO @ Tue, 14 Jul 2020 08:01:56: 8000000 INFO @ Tue, 14 Jul 2020 08:02:00: 2000000 INFO @ Tue, 14 Jul 2020 08:02:01: 9000000 INFO @ Tue, 14 Jul 2020 08:02:05: 10000000 INFO @ Tue, 14 Jul 2020 08:02:06: 3000000 INFO @ Tue, 14 Jul 2020 08:02:10: 11000000 INFO @ Tue, 14 Jul 2020 08:02:12: 4000000 INFO @ Tue, 14 Jul 2020 08:02:15: 12000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:02:18: 5000000 INFO @ Tue, 14 Jul 2020 08:02:19: 13000000 INFO @ Tue, 14 Jul 2020 08:02:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.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 @ Tue, 14 Jul 2020 08:02:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:02:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:02:24: 14000000 INFO @ Tue, 14 Jul 2020 08:02:24: 1000000 INFO @ Tue, 14 Jul 2020 08:02:25: 6000000 INFO @ Tue, 14 Jul 2020 08:02:29: 15000000 INFO @ Tue, 14 Jul 2020 08:02:29: 2000000 INFO @ Tue, 14 Jul 2020 08:02:31: 7000000 INFO @ Tue, 14 Jul 2020 08:02:34: 16000000 INFO @ Tue, 14 Jul 2020 08:02:34: 3000000 INFO @ Tue, 14 Jul 2020 08:02:38: 8000000 INFO @ Tue, 14 Jul 2020 08:02:38: 17000000 INFO @ Tue, 14 Jul 2020 08:02:38: 4000000 INFO @ Tue, 14 Jul 2020 08:02:42: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:02:42: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:02:42: #1 total tags in treatment: 17643808 INFO @ Tue, 14 Jul 2020 08:02:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:02:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:02:42: #1 tags after filtering in treatment: 17643808 INFO @ Tue, 14 Jul 2020 08:02:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:02:42: #1 finished! INFO @ Tue, 14 Jul 2020 08:02:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:02:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:02:43: #2 number of paired peaks: 313 WARNING @ Tue, 14 Jul 2020 08:02:43: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 14 Jul 2020 08:02:43: start model_add_line... INFO @ Tue, 14 Jul 2020 08:02:43: 5000000 INFO @ Tue, 14 Jul 2020 08:02:43: start X-correlation... INFO @ Tue, 14 Jul 2020 08:02:43: end of X-cor INFO @ Tue, 14 Jul 2020 08:02:43: #2 finished! INFO @ Tue, 14 Jul 2020 08:02:43: #2 predicted fragment length is 41 bps INFO @ Tue, 14 Jul 2020 08:02:43: #2 alternative fragment length(s) may be 2,41,562,595 bps INFO @ Tue, 14 Jul 2020 08:02:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.05_model.r WARNING @ Tue, 14 Jul 2020 08:02:43: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:02:43: #2 You may need to consider one of the other alternative d(s): 2,41,562,595 WARNING @ Tue, 14 Jul 2020 08:02:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:02:43: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:02:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:02:44: 9000000 INFO @ Tue, 14 Jul 2020 08:02:48: 6000000 INFO @ Tue, 14 Jul 2020 08:02:51: 10000000 INFO @ Tue, 14 Jul 2020 08:02:52: 7000000 INFO @ Tue, 14 Jul 2020 08:02:57: 8000000 INFO @ Tue, 14 Jul 2020 08:02:58: 11000000 INFO @ Tue, 14 Jul 2020 08:03:02: 9000000 INFO @ Tue, 14 Jul 2020 08:03:05: 12000000 INFO @ Tue, 14 Jul 2020 08:03:06: 10000000 INFO @ Tue, 14 Jul 2020 08:03:11: 11000000 INFO @ Tue, 14 Jul 2020 08:03:12: 13000000 INFO @ Tue, 14 Jul 2020 08:03:12: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:03:15: 12000000 INFO @ Tue, 14 Jul 2020 08:03:18: 14000000 INFO @ Tue, 14 Jul 2020 08:03:20: 13000000 INFO @ Tue, 14 Jul 2020 08:03:25: 14000000 INFO @ Tue, 14 Jul 2020 08:03:25: 15000000 INFO @ Tue, 14 Jul 2020 08:03:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:03:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:03:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.05_summits.bed INFO @ Tue, 14 Jul 2020 08:03:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (856 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:03:29: 15000000 INFO @ Tue, 14 Jul 2020 08:03:31: 16000000 INFO @ Tue, 14 Jul 2020 08:03:34: 16000000 INFO @ Tue, 14 Jul 2020 08:03:37: 17000000 INFO @ Tue, 14 Jul 2020 08:03:39: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:03:42: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:03:42: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:03:42: #1 total tags in treatment: 17643808 INFO @ Tue, 14 Jul 2020 08:03:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:03:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:03:42: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:03:42: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:03:42: #1 total tags in treatment: 17643808 INFO @ Tue, 14 Jul 2020 08:03:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:03:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:03:42: #1 tags after filtering in treatment: 17643808 INFO @ Tue, 14 Jul 2020 08:03:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:03:42: #1 finished! INFO @ Tue, 14 Jul 2020 08:03:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:03:42: #1 tags after filtering in treatment: 17643808 INFO @ Tue, 14 Jul 2020 08:03:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:03:42: #1 finished! INFO @ Tue, 14 Jul 2020 08:03:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:03:43: #2 number of paired peaks: 313 WARNING @ Tue, 14 Jul 2020 08:03:43: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 14 Jul 2020 08:03:43: start model_add_line... INFO @ Tue, 14 Jul 2020 08:03:43: start X-correlation... INFO @ Tue, 14 Jul 2020 08:03:43: end of X-cor INFO @ Tue, 14 Jul 2020 08:03:43: #2 finished! INFO @ Tue, 14 Jul 2020 08:03:43: #2 predicted fragment length is 41 bps INFO @ Tue, 14 Jul 2020 08:03:43: #2 alternative fragment length(s) may be 2,41,562,595 bps INFO @ Tue, 14 Jul 2020 08:03:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.20_model.r WARNING @ Tue, 14 Jul 2020 08:03:43: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:03:43: #2 You may need to consider one of the other alternative d(s): 2,41,562,595 WARNING @ Tue, 14 Jul 2020 08:03:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:03:43: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:03:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:03:43: #2 number of paired peaks: 313 WARNING @ Tue, 14 Jul 2020 08:03:43: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 14 Jul 2020 08:03:43: start model_add_line... INFO @ Tue, 14 Jul 2020 08:03:44: start X-correlation... INFO @ Tue, 14 Jul 2020 08:03:44: end of X-cor INFO @ Tue, 14 Jul 2020 08:03:44: #2 finished! INFO @ Tue, 14 Jul 2020 08:03:44: #2 predicted fragment length is 41 bps INFO @ Tue, 14 Jul 2020 08:03:44: #2 alternative fragment length(s) may be 2,41,562,595 bps INFO @ Tue, 14 Jul 2020 08:03:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.10_model.r WARNING @ Tue, 14 Jul 2020 08:03:44: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:03:44: #2 You may need to consider one of the other alternative d(s): 2,41,562,595 WARNING @ Tue, 14 Jul 2020 08:03:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:03:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:03:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:04:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:04:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:04:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:04:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.20_summits.bed INFO @ Tue, 14 Jul 2020 08:04:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (233 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:04:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:04:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7630546/SRX7630546.10_summits.bed INFO @ Tue, 14 Jul 2020 08:04:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (512 records, 4 fields): 11 millis CompletedMACS2peakCalling