Job ID = 14170776 SRX = SRX8689005 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: 00:04:46 16976515 reads; of these: 16976515 (100.00%) were unpaired; of these: 531849 (3.13%) aligned 0 times 11951585 (70.40%) aligned exactly 1 time 4493081 (26.47%) aligned >1 times 96.87% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 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] 1671156 / 16444666 = 0.1016 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 08:43:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.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 08:43:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:43:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:43:40: 1000000 INFO @ Sat, 11 Dec 2021 08:43:46: 2000000 INFO @ Sat, 11 Dec 2021 08:43:52: 3000000 INFO @ Sat, 11 Dec 2021 08:43:57: 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 08:44:03: 5000000 INFO @ Sat, 11 Dec 2021 08:44:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.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 08:44:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:44:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:44:09: 6000000 INFO @ Sat, 11 Dec 2021 08:44:10: 1000000 INFO @ Sat, 11 Dec 2021 08:44:15: 7000000 INFO @ Sat, 11 Dec 2021 08:44:16: 2000000 INFO @ Sat, 11 Dec 2021 08:44:20: 8000000 INFO @ Sat, 11 Dec 2021 08:44:21: 3000000 INFO @ Sat, 11 Dec 2021 08:44:26: 9000000 INFO @ Sat, 11 Dec 2021 08:44:27: 4000000 INFO @ Sat, 11 Dec 2021 08:44:32: 10000000 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 08:44:33: 5000000 INFO @ Sat, 11 Dec 2021 08:44:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.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 08:44:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:44:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:44:38: 11000000 INFO @ Sat, 11 Dec 2021 08:44:39: 6000000 INFO @ Sat, 11 Dec 2021 08:44:40: 1000000 INFO @ Sat, 11 Dec 2021 08:44:44: 12000000 INFO @ Sat, 11 Dec 2021 08:44:45: 7000000 INFO @ Sat, 11 Dec 2021 08:44:47: 2000000 INFO @ Sat, 11 Dec 2021 08:44:51: 13000000 INFO @ Sat, 11 Dec 2021 08:44:51: 8000000 INFO @ Sat, 11 Dec 2021 08:44:53: 3000000 INFO @ Sat, 11 Dec 2021 08:44:57: 14000000 INFO @ Sat, 11 Dec 2021 08:44:58: 9000000 INFO @ Sat, 11 Dec 2021 08:45:00: 4000000 INFO @ Sat, 11 Dec 2021 08:45:02: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:45:02: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:45:02: #1 total tags in treatment: 14773510 INFO @ Sat, 11 Dec 2021 08:45:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:45:02: #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 08:45:02: #1 tags after filtering in treatment: 14773420 INFO @ Sat, 11 Dec 2021 08:45:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:45:02: #1 finished! INFO @ Sat, 11 Dec 2021 08:45:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:45:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:45:04: #2 number of paired peaks: 741 WARNING @ Sat, 11 Dec 2021 08:45:04: Fewer paired peaks (741) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 741 pairs to build model! INFO @ Sat, 11 Dec 2021 08:45:04: start model_add_line... INFO @ Sat, 11 Dec 2021 08:45:04: start X-correlation... INFO @ Sat, 11 Dec 2021 08:45:04: end of X-cor INFO @ Sat, 11 Dec 2021 08:45:04: #2 finished! INFO @ Sat, 11 Dec 2021 08:45:04: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 08:45:04: #2 alternative fragment length(s) may be 4,47 bps INFO @ Sat, 11 Dec 2021 08:45:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.05_model.r WARNING @ Sat, 11 Dec 2021 08:45:04: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:45:04: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Sat, 11 Dec 2021 08:45:04: #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 08:45:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:45:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:45:04: 10000000 INFO @ Sat, 11 Dec 2021 08:45:06: 5000000 INFO @ Sat, 11 Dec 2021 08:45:10: 11000000 INFO @ Sat, 11 Dec 2021 08:45:13: 6000000 INFO @ Sat, 11 Dec 2021 08:45:17: 12000000 INFO @ Sat, 11 Dec 2021 08:45:19: 7000000 INFO @ Sat, 11 Dec 2021 08:45:23: 13000000 INFO @ Sat, 11 Dec 2021 08:45:26: 8000000 INFO @ Sat, 11 Dec 2021 08:45:29: 14000000 INFO @ Sat, 11 Dec 2021 08:45:32: 9000000 INFO @ Sat, 11 Dec 2021 08:45:34: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:45:34: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:45:34: #1 total tags in treatment: 14773510 INFO @ Sat, 11 Dec 2021 08:45:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:45:34: #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 08:45:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:45:34: #1 tags after filtering in treatment: 14773420 INFO @ Sat, 11 Dec 2021 08:45:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:45:34: #1 finished! INFO @ Sat, 11 Dec 2021 08:45:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:45:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:45:35: #2 number of paired peaks: 741 WARNING @ Sat, 11 Dec 2021 08:45:35: Fewer paired peaks (741) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 741 pairs to build model! INFO @ Sat, 11 Dec 2021 08:45:35: start model_add_line... INFO @ Sat, 11 Dec 2021 08:45:36: start X-correlation... INFO @ Sat, 11 Dec 2021 08:45:36: end of X-cor INFO @ Sat, 11 Dec 2021 08:45:36: #2 finished! INFO @ Sat, 11 Dec 2021 08:45:36: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 08:45:36: #2 alternative fragment length(s) may be 4,47 bps INFO @ Sat, 11 Dec 2021 08:45:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.10_model.r WARNING @ Sat, 11 Dec 2021 08:45:36: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:45:36: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Sat, 11 Dec 2021 08:45:36: #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 08:45:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:45:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:45:38: 10000000 INFO @ Sat, 11 Dec 2021 08:45:44: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:45:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:45:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:45:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.05_summits.bed INFO @ Sat, 11 Dec 2021 08:45:48: Done! pass1 - making usageList (664 chroms): 2 millis pass2 - checking and writing primary data (2990 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:45:51: 12000000 INFO @ Sat, 11 Dec 2021 08:45:56: 13000000 INFO @ Sat, 11 Dec 2021 08:46:02: 14000000 INFO @ Sat, 11 Dec 2021 08:46:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:46:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:46:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:46:07: #1 total tags in treatment: 14773510 INFO @ Sat, 11 Dec 2021 08:46:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:46:07: #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 08:46:08: #1 tags after filtering in treatment: 14773420 INFO @ Sat, 11 Dec 2021 08:46:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:46:08: #1 finished! INFO @ Sat, 11 Dec 2021 08:46:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:46:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:46:09: #2 number of paired peaks: 741 WARNING @ Sat, 11 Dec 2021 08:46:09: Fewer paired peaks (741) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 741 pairs to build model! INFO @ Sat, 11 Dec 2021 08:46:09: start model_add_line... INFO @ Sat, 11 Dec 2021 08:46:09: start X-correlation... INFO @ Sat, 11 Dec 2021 08:46:09: end of X-cor INFO @ Sat, 11 Dec 2021 08:46:09: #2 finished! INFO @ Sat, 11 Dec 2021 08:46:09: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 08:46:09: #2 alternative fragment length(s) may be 4,47 bps INFO @ Sat, 11 Dec 2021 08:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.20_model.r WARNING @ Sat, 11 Dec 2021 08:46:09: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:46:09: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Sat, 11 Dec 2021 08:46:09: #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 08:46:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:46:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:46:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:46:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.10_summits.bed INFO @ Sat, 11 Dec 2021 08:46:18: Done! pass1 - making usageList (578 chroms): 1 millis pass2 - checking and writing primary data (2287 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:46:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689005/SRX8689005.20_summits.bed INFO @ Sat, 11 Dec 2021 08:46:53: Done! pass1 - making usageList (383 chroms): 1 millis pass2 - checking and writing primary data (812 records, 4 fields): 13 millis CompletedMACS2peakCalling