Job ID = 12265574 SRX = SRX6817540 Genome = dm6 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: 00:20:36 31864775 reads; of these: 31864775 (100.00%) were unpaired; of these: 19243298 (60.39%) aligned 0 times 9523906 (29.89%) aligned exactly 1 time 3097571 (9.72%) aligned >1 times 39.61% overall alignment rate Time searching: 00:20:36 Overall time: 00:20:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2219097 / 12621477 = 0.1758 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 08:04:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.bam'] # control file = None # effective genome size = 1.20e+08 # 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 08:04:35: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:04:35: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:04:43: 1000000 INFO @ Sat, 03 Apr 2021 08:04:50: 2000000 INFO @ Sat, 03 Apr 2021 08:04:58: 3000000 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 08:05:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.bam'] # control file = None # effective genome size = 1.20e+08 # 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 08:05:05: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:05:05: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:05:06: 4000000 INFO @ Sat, 03 Apr 2021 08:05:13: 1000000 INFO @ Sat, 03 Apr 2021 08:05:15: 5000000 INFO @ Sat, 03 Apr 2021 08:05:21: 2000000 INFO @ Sat, 03 Apr 2021 08:05:23: 6000000 INFO @ Sat, 03 Apr 2021 08:05:29: 3000000 INFO @ Sat, 03 Apr 2021 08:05:31: 7000000 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 08:05:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.bam'] # control file = None # effective genome size = 1.20e+08 # 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 08:05:35: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:05:35: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:05:37: 4000000 INFO @ Sat, 03 Apr 2021 08:05:39: 8000000 INFO @ Sat, 03 Apr 2021 08:05:44: 1000000 INFO @ Sat, 03 Apr 2021 08:05:47: 5000000 INFO @ Sat, 03 Apr 2021 08:05:48: 9000000 INFO @ Sat, 03 Apr 2021 08:05:53: 2000000 INFO @ Sat, 03 Apr 2021 08:05:56: 10000000 INFO @ Sat, 03 Apr 2021 08:05:56: 6000000 INFO @ Sat, 03 Apr 2021 08:06:00: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 08:06:00: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 08:06:00: #1 total tags in treatment: 10402380 INFO @ Sat, 03 Apr 2021 08:06:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:06:00: #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 08:06:00: #1 tags after filtering in treatment: 10402367 INFO @ Sat, 03 Apr 2021 08:06:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:06:00: #1 finished! INFO @ Sat, 03 Apr 2021 08:06:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:06:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:06:01: #2 number of paired peaks: 259 WARNING @ Sat, 03 Apr 2021 08:06:01: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Sat, 03 Apr 2021 08:06:01: start model_add_line... INFO @ Sat, 03 Apr 2021 08:06:01: start X-correlation... INFO @ Sat, 03 Apr 2021 08:06:01: end of X-cor INFO @ Sat, 03 Apr 2021 08:06:01: #2 finished! INFO @ Sat, 03 Apr 2021 08:06:01: #2 predicted fragment length is 87 bps INFO @ Sat, 03 Apr 2021 08:06:01: #2 alternative fragment length(s) may be 4,87,559,581,597 bps INFO @ Sat, 03 Apr 2021 08:06:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.05_model.r WARNING @ Sat, 03 Apr 2021 08:06:01: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:06:01: #2 You may need to consider one of the other alternative d(s): 4,87,559,581,597 WARNING @ Sat, 03 Apr 2021 08:06:01: #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 08:06:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:06:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:06:02: 3000000 INFO @ Sat, 03 Apr 2021 08:06:05: 7000000 INFO @ Sat, 03 Apr 2021 08:06:11: 4000000 INFO @ Sat, 03 Apr 2021 08:06:14: 8000000 INFO @ Sat, 03 Apr 2021 08:06:20: 5000000 INFO @ Sat, 03 Apr 2021 08:06:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:06:24: 9000000 INFO @ Sat, 03 Apr 2021 08:06:29: 6000000 INFO @ Sat, 03 Apr 2021 08:06:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:06:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:06:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.05_summits.bed INFO @ Sat, 03 Apr 2021 08:06:31: Done! pass1 - making usageList (629 chroms): 2 millis pass2 - checking and writing primary data (2869 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:06:33: 10000000 INFO @ Sat, 03 Apr 2021 08:06:37: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 08:06:37: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 08:06:37: #1 total tags in treatment: 10402380 INFO @ Sat, 03 Apr 2021 08:06:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:06:37: #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 08:06:37: 7000000 INFO @ Sat, 03 Apr 2021 08:06:38: #1 tags after filtering in treatment: 10402367 INFO @ Sat, 03 Apr 2021 08:06:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:06:38: #1 finished! INFO @ Sat, 03 Apr 2021 08:06:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:06:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:06:38: #2 number of paired peaks: 259 WARNING @ Sat, 03 Apr 2021 08:06:38: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Sat, 03 Apr 2021 08:06:38: start model_add_line... INFO @ Sat, 03 Apr 2021 08:06:38: start X-correlation... INFO @ Sat, 03 Apr 2021 08:06:38: end of X-cor INFO @ Sat, 03 Apr 2021 08:06:38: #2 finished! INFO @ Sat, 03 Apr 2021 08:06:38: #2 predicted fragment length is 87 bps INFO @ Sat, 03 Apr 2021 08:06:38: #2 alternative fragment length(s) may be 4,87,559,581,597 bps INFO @ Sat, 03 Apr 2021 08:06:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.10_model.r WARNING @ Sat, 03 Apr 2021 08:06:38: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:06:38: #2 You may need to consider one of the other alternative d(s): 4,87,559,581,597 WARNING @ Sat, 03 Apr 2021 08:06:38: #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 08:06:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:06:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:06:45: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:06:53: 9000000 INFO @ Sat, 03 Apr 2021 08:06:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:07:01: 10000000 INFO @ Sat, 03 Apr 2021 08:07:05: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 08:07:05: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 08:07:05: #1 total tags in treatment: 10402380 INFO @ Sat, 03 Apr 2021 08:07:05: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:07:05: #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 08:07:06: #1 tags after filtering in treatment: 10402367 INFO @ Sat, 03 Apr 2021 08:07:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:07:06: #1 finished! INFO @ Sat, 03 Apr 2021 08:07:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:07:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:07:07: #2 number of paired peaks: 259 WARNING @ Sat, 03 Apr 2021 08:07:07: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Sat, 03 Apr 2021 08:07:07: start model_add_line... INFO @ Sat, 03 Apr 2021 08:07:07: start X-correlation... INFO @ Sat, 03 Apr 2021 08:07:07: end of X-cor INFO @ Sat, 03 Apr 2021 08:07:07: #2 finished! INFO @ Sat, 03 Apr 2021 08:07:07: #2 predicted fragment length is 87 bps INFO @ Sat, 03 Apr 2021 08:07:07: #2 alternative fragment length(s) may be 4,87,559,581,597 bps INFO @ Sat, 03 Apr 2021 08:07:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.20_model.r WARNING @ Sat, 03 Apr 2021 08:07:07: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:07:07: #2 You may need to consider one of the other alternative d(s): 4,87,559,581,597 WARNING @ Sat, 03 Apr 2021 08:07:07: #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 08:07:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:07:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:07:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:07:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:07:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.10_summits.bed INFO @ Sat, 03 Apr 2021 08:07:08: Done! pass1 - making usageList (455 chroms): 1 millis pass2 - checking and writing primary data (1099 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:07:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:07:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:07:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:07:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6817540/SRX6817540.20_summits.bed INFO @ Sat, 03 Apr 2021 08:07:36: Done! pass1 - making usageList (185 chroms): 1 millis pass2 - checking and writing primary data (277 records, 4 fields): 13 millis CompletedMACS2peakCalling