Job ID = 14170896 SRX = SRX8689039 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: 00:04:32 16670807 reads; of these: 16670807 (100.00%) were unpaired; of these: 465465 (2.79%) aligned 0 times 11824661 (70.93%) aligned exactly 1 time 4380681 (26.28%) aligned >1 times 97.21% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 1615423 / 16205342 = 0.0997 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 @ Sat, 11 Dec 2021 09:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.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, 11 Dec 2021 09:06:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:06:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:06:06: 1000000 INFO @ Sat, 11 Dec 2021 09:06:12: 2000000 INFO @ Sat, 11 Dec 2021 09:06:18: 3000000 INFO @ Sat, 11 Dec 2021 09:06:25: 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 @ Sat, 11 Dec 2021 09:06:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.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, 11 Dec 2021 09:06:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:06:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:06:31: 5000000 INFO @ Sat, 11 Dec 2021 09:06:37: 1000000 INFO @ Sat, 11 Dec 2021 09:06:37: 6000000 INFO @ Sat, 11 Dec 2021 09:06:43: 2000000 INFO @ Sat, 11 Dec 2021 09:06:43: 7000000 INFO @ Sat, 11 Dec 2021 09:06:49: 3000000 INFO @ Sat, 11 Dec 2021 09:06:50: 8000000 INFO @ Sat, 11 Dec 2021 09:06:56: 4000000 INFO @ Sat, 11 Dec 2021 09:06:56: 9000000 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 @ Sat, 11 Dec 2021 09:07:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.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, 11 Dec 2021 09:07:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:07:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:07:02: 5000000 INFO @ Sat, 11 Dec 2021 09:07:02: 10000000 INFO @ Sat, 11 Dec 2021 09:07:06: 1000000 INFO @ Sat, 11 Dec 2021 09:07:08: 6000000 INFO @ Sat, 11 Dec 2021 09:07:09: 11000000 INFO @ Sat, 11 Dec 2021 09:07:11: 2000000 INFO @ Sat, 11 Dec 2021 09:07:15: 7000000 INFO @ Sat, 11 Dec 2021 09:07:15: 12000000 INFO @ Sat, 11 Dec 2021 09:07:17: 3000000 INFO @ Sat, 11 Dec 2021 09:07:21: 8000000 INFO @ Sat, 11 Dec 2021 09:07:22: 13000000 INFO @ Sat, 11 Dec 2021 09:07:22: 4000000 INFO @ Sat, 11 Dec 2021 09:07:27: 9000000 INFO @ Sat, 11 Dec 2021 09:07:28: 5000000 INFO @ Sat, 11 Dec 2021 09:07:28: 14000000 INFO @ Sat, 11 Dec 2021 09:07:32: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:07:32: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:07:32: #1 total tags in treatment: 14589919 INFO @ Sat, 11 Dec 2021 09:07:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:07:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:07:33: #1 tags after filtering in treatment: 14589836 INFO @ Sat, 11 Dec 2021 09:07:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:07:33: #1 finished! INFO @ Sat, 11 Dec 2021 09:07:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:07:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:07:34: 6000000 INFO @ Sat, 11 Dec 2021 09:07:34: 10000000 INFO @ Sat, 11 Dec 2021 09:07:34: #2 number of paired peaks: 722 WARNING @ Sat, 11 Dec 2021 09:07:34: Fewer paired peaks (722) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 722 pairs to build model! INFO @ Sat, 11 Dec 2021 09:07:34: start model_add_line... INFO @ Sat, 11 Dec 2021 09:07:34: start X-correlation... INFO @ Sat, 11 Dec 2021 09:07:34: end of X-cor INFO @ Sat, 11 Dec 2021 09:07:34: #2 finished! INFO @ Sat, 11 Dec 2021 09:07:34: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:07:34: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 11 Dec 2021 09:07:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.05_model.r WARNING @ Sat, 11 Dec 2021 09:07:34: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:07:34: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 11 Dec 2021 09:07:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:07:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:07:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:07:39: 7000000 INFO @ Sat, 11 Dec 2021 09:07:40: 11000000 INFO @ Sat, 11 Dec 2021 09:07:44: 8000000 INFO @ Sat, 11 Dec 2021 09:07:47: 12000000 INFO @ Sat, 11 Dec 2021 09:07:50: 9000000 INFO @ Sat, 11 Dec 2021 09:07:53: 13000000 INFO @ Sat, 11 Dec 2021 09:07:55: 10000000 INFO @ Sat, 11 Dec 2021 09:07:59: 14000000 INFO @ Sat, 11 Dec 2021 09:08:01: 11000000 INFO @ Sat, 11 Dec 2021 09:08:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:08:03: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:08:03: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:08:03: #1 total tags in treatment: 14589919 INFO @ Sat, 11 Dec 2021 09:08:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:08:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:08:03: #1 tags after filtering in treatment: 14589836 INFO @ Sat, 11 Dec 2021 09:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:08:03: #1 finished! INFO @ Sat, 11 Dec 2021 09:08:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:08:04: #2 number of paired peaks: 722 WARNING @ Sat, 11 Dec 2021 09:08:04: Fewer paired peaks (722) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 722 pairs to build model! INFO @ Sat, 11 Dec 2021 09:08:04: start model_add_line... INFO @ Sat, 11 Dec 2021 09:08:05: start X-correlation... INFO @ Sat, 11 Dec 2021 09:08:05: end of X-cor INFO @ Sat, 11 Dec 2021 09:08:05: #2 finished! INFO @ Sat, 11 Dec 2021 09:08:05: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:08:05: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 11 Dec 2021 09:08:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.10_model.r WARNING @ Sat, 11 Dec 2021 09:08:05: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:08:05: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 11 Dec 2021 09:08:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:08:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:08:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:08:06: 12000000 INFO @ Sat, 11 Dec 2021 09:08:11: 13000000 INFO @ Sat, 11 Dec 2021 09:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.05_summits.bed INFO @ Sat, 11 Dec 2021 09:08:15: Done! pass1 - making usageList (696 chroms): 2 millis pass2 - checking and writing primary data (3064 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:08:17: 14000000 INFO @ Sat, 11 Dec 2021 09:08:20: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:08:20: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:08:20: #1 total tags in treatment: 14589919 INFO @ Sat, 11 Dec 2021 09:08:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:08:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:08:20: #1 tags after filtering in treatment: 14589836 INFO @ Sat, 11 Dec 2021 09:08:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:08:20: #1 finished! INFO @ Sat, 11 Dec 2021 09:08:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:08:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:08:21: #2 number of paired peaks: 722 WARNING @ Sat, 11 Dec 2021 09:08:21: Fewer paired peaks (722) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 722 pairs to build model! INFO @ Sat, 11 Dec 2021 09:08:21: start model_add_line... INFO @ Sat, 11 Dec 2021 09:08:21: start X-correlation... INFO @ Sat, 11 Dec 2021 09:08:21: end of X-cor INFO @ Sat, 11 Dec 2021 09:08:21: #2 finished! INFO @ Sat, 11 Dec 2021 09:08:21: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:08:21: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 11 Dec 2021 09:08:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.20_model.r WARNING @ Sat, 11 Dec 2021 09:08:21: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:08:21: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 11 Dec 2021 09:08:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:08:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:08:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:08:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:08:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:08:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:08:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.10_summits.bed INFO @ Sat, 11 Dec 2021 09:08:44: Done! pass1 - making usageList (592 chroms): 1 millis pass2 - checking and writing primary data (2159 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:08:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:09:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:09:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:09:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689039/SRX8689039.20_summits.bed INFO @ Sat, 11 Dec 2021 09:09:02: Done! pass1 - making usageList (376 chroms): 1 millis pass2 - checking and writing primary data (838 records, 4 fields): 10 millis CompletedMACS2peakCalling