Job ID = 14171763 SRX = SRX9986141 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: 00:00:01 Multiseed full-index search: 00:09:24 27285086 reads; of these: 27285086 (100.00%) were unpaired; of these: 1641829 (6.02%) aligned 0 times 16230880 (59.49%) aligned exactly 1 time 9412377 (34.50%) aligned >1 times 93.98% overall alignment rate Time searching: 00:09:25 Overall time: 00:09:25 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 12 files... [bam_rmdupse_core] 6545654 / 25643257 = 0.2553 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 13:01:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.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 13:01:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:01:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:01:11: 1000000 INFO @ Sat, 11 Dec 2021 13:01:21: 2000000 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 13:01:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.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 13:01:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:01:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:01:31: 3000000 INFO @ Sat, 11 Dec 2021 13:01:38: 1000000 INFO @ Sat, 11 Dec 2021 13:01:42: 4000000 INFO @ Sat, 11 Dec 2021 13:01:46: 2000000 INFO @ Sat, 11 Dec 2021 13:01:52: 5000000 INFO @ Sat, 11 Dec 2021 13:01:55: 3000000 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 13:01:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.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 13:01:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:01:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:02:03: 6000000 INFO @ Sat, 11 Dec 2021 13:02:03: 4000000 INFO @ Sat, 11 Dec 2021 13:02:07: 1000000 INFO @ Sat, 11 Dec 2021 13:02:11: 5000000 INFO @ Sat, 11 Dec 2021 13:02:14: 7000000 INFO @ Sat, 11 Dec 2021 13:02:16: 2000000 INFO @ Sat, 11 Dec 2021 13:02:20: 6000000 INFO @ Sat, 11 Dec 2021 13:02:24: 3000000 INFO @ Sat, 11 Dec 2021 13:02:24: 8000000 INFO @ Sat, 11 Dec 2021 13:02:29: 7000000 INFO @ Sat, 11 Dec 2021 13:02:32: 4000000 INFO @ Sat, 11 Dec 2021 13:02:35: 9000000 INFO @ Sat, 11 Dec 2021 13:02:37: 8000000 INFO @ Sat, 11 Dec 2021 13:02:41: 5000000 INFO @ Sat, 11 Dec 2021 13:02:45: 10000000 INFO @ Sat, 11 Dec 2021 13:02:46: 9000000 INFO @ Sat, 11 Dec 2021 13:02:49: 6000000 INFO @ Sat, 11 Dec 2021 13:02:55: 10000000 INFO @ Sat, 11 Dec 2021 13:02:55: 11000000 INFO @ Sat, 11 Dec 2021 13:02:57: 7000000 INFO @ Sat, 11 Dec 2021 13:03:04: 11000000 INFO @ Sat, 11 Dec 2021 13:03:05: 8000000 INFO @ Sat, 11 Dec 2021 13:03:06: 12000000 INFO @ Sat, 11 Dec 2021 13:03:12: 12000000 INFO @ Sat, 11 Dec 2021 13:03:14: 9000000 INFO @ Sat, 11 Dec 2021 13:03:16: 13000000 INFO @ Sat, 11 Dec 2021 13:03:21: 13000000 INFO @ Sat, 11 Dec 2021 13:03:23: 10000000 INFO @ Sat, 11 Dec 2021 13:03:26: 14000000 INFO @ Sat, 11 Dec 2021 13:03:30: 14000000 INFO @ Sat, 11 Dec 2021 13:03:31: 11000000 INFO @ Sat, 11 Dec 2021 13:03:37: 15000000 INFO @ Sat, 11 Dec 2021 13:03:38: 15000000 INFO @ Sat, 11 Dec 2021 13:03:39: 12000000 INFO @ Sat, 11 Dec 2021 13:03:47: 16000000 INFO @ Sat, 11 Dec 2021 13:03:48: 16000000 INFO @ Sat, 11 Dec 2021 13:03:48: 13000000 INFO @ Sat, 11 Dec 2021 13:03:56: 14000000 INFO @ Sat, 11 Dec 2021 13:03:56: 17000000 INFO @ Sat, 11 Dec 2021 13:03:59: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:04:04: 15000000 INFO @ Sat, 11 Dec 2021 13:04:04: 18000000 INFO @ Sat, 11 Dec 2021 13:04:09: 18000000 INFO @ Sat, 11 Dec 2021 13:04:13: 16000000 INFO @ Sat, 11 Dec 2021 13:04:13: 19000000 INFO @ Sat, 11 Dec 2021 13:04:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:04:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:04:14: #1 total tags in treatment: 19097603 INFO @ Sat, 11 Dec 2021 13:04:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:04:14: #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 13:04:15: #1 tags after filtering in treatment: 19097539 INFO @ Sat, 11 Dec 2021 13:04:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:04:15: #1 finished! INFO @ Sat, 11 Dec 2021 13:04:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:04:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:04:17: #2 number of paired peaks: 645 WARNING @ Sat, 11 Dec 2021 13:04:17: Fewer paired peaks (645) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 645 pairs to build model! INFO @ Sat, 11 Dec 2021 13:04:17: start model_add_line... INFO @ Sat, 11 Dec 2021 13:04:17: start X-correlation... INFO @ Sat, 11 Dec 2021 13:04:17: end of X-cor INFO @ Sat, 11 Dec 2021 13:04:17: #2 finished! INFO @ Sat, 11 Dec 2021 13:04:17: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 13:04:17: #2 alternative fragment length(s) may be 1,51,534 bps INFO @ Sat, 11 Dec 2021 13:04:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.10_model.r WARNING @ Sat, 11 Dec 2021 13:04:17: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:04:17: #2 You may need to consider one of the other alternative d(s): 1,51,534 WARNING @ Sat, 11 Dec 2021 13:04:17: #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 13:04:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:04:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:04:20: 19000000 INFO @ Sat, 11 Dec 2021 13:04:21: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:04:21: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:04:21: #1 total tags in treatment: 19097603 INFO @ Sat, 11 Dec 2021 13:04:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:04:21: #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 13:04:22: 17000000 INFO @ Sat, 11 Dec 2021 13:04:22: #1 tags after filtering in treatment: 19097539 INFO @ Sat, 11 Dec 2021 13:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:04:22: #1 finished! INFO @ Sat, 11 Dec 2021 13:04:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:04:24: #2 number of paired peaks: 645 WARNING @ Sat, 11 Dec 2021 13:04:24: Fewer paired peaks (645) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 645 pairs to build model! INFO @ Sat, 11 Dec 2021 13:04:24: start model_add_line... INFO @ Sat, 11 Dec 2021 13:04:24: start X-correlation... INFO @ Sat, 11 Dec 2021 13:04:24: end of X-cor INFO @ Sat, 11 Dec 2021 13:04:24: #2 finished! INFO @ Sat, 11 Dec 2021 13:04:24: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 13:04:24: #2 alternative fragment length(s) may be 1,51,534 bps INFO @ Sat, 11 Dec 2021 13:04:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.05_model.r WARNING @ Sat, 11 Dec 2021 13:04:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:04:24: #2 You may need to consider one of the other alternative d(s): 1,51,534 WARNING @ Sat, 11 Dec 2021 13:04:24: #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 13:04:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:04:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:04:29: 18000000 INFO @ Sat, 11 Dec 2021 13:04:38: 19000000 INFO @ Sat, 11 Dec 2021 13:04:39: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:04:39: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:04:39: #1 total tags in treatment: 19097603 INFO @ Sat, 11 Dec 2021 13:04:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:04:39: #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 13:04:39: #1 tags after filtering in treatment: 19097539 INFO @ Sat, 11 Dec 2021 13:04:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:04:39: #1 finished! INFO @ Sat, 11 Dec 2021 13:04:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:04:41: #2 number of paired peaks: 645 WARNING @ Sat, 11 Dec 2021 13:04:41: Fewer paired peaks (645) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 645 pairs to build model! INFO @ Sat, 11 Dec 2021 13:04:41: start model_add_line... INFO @ Sat, 11 Dec 2021 13:04:41: start X-correlation... INFO @ Sat, 11 Dec 2021 13:04:41: end of X-cor INFO @ Sat, 11 Dec 2021 13:04:41: #2 finished! INFO @ Sat, 11 Dec 2021 13:04:41: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 13:04:41: #2 alternative fragment length(s) may be 1,51,534 bps INFO @ Sat, 11 Dec 2021 13:04:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.20_model.r WARNING @ Sat, 11 Dec 2021 13:04:41: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:04:41: #2 You may need to consider one of the other alternative d(s): 1,51,534 WARNING @ Sat, 11 Dec 2021 13:04:41: #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 13:04:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:04:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:05:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:05:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:05:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:05:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:05:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:05:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.10_summits.bed INFO @ Sat, 11 Dec 2021 13:05:33: Done! pass1 - making usageList (514 chroms): 3 millis pass2 - checking and writing primary data (2035 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:05:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:05:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:05:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.05_summits.bed INFO @ Sat, 11 Dec 2021 13:05:39: Done! pass1 - making usageList (642 chroms): 3 millis pass2 - checking and writing primary data (2885 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:05:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:05:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:05:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986141/SRX9986141.20_summits.bed INFO @ Sat, 11 Dec 2021 13:05:56: Done! pass1 - making usageList (285 chroms): 1 millis pass2 - checking and writing primary data (646 records, 4 fields): 20 millis CompletedMACS2peakCalling