Job ID = 6529215 SRX = SRX066250 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: 00:04:53 19763112 reads; of these: 19763112 (100.00%) were unpaired; of these: 676487 (3.42%) aligned 0 times 14483700 (73.29%) aligned exactly 1 time 4602925 (23.29%) aligned >1 times 96.58% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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] 2894373 / 19086625 = 0.1516 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, 30 Jun 2020 01:46:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.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 @ Tue, 30 Jun 2020 01:46:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:46:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:46:21: 1000000 INFO @ Tue, 30 Jun 2020 01:46:26: 2000000 INFO @ Tue, 30 Jun 2020 01:46:31: 3000000 INFO @ Tue, 30 Jun 2020 01:46:36: 4000000 INFO @ Tue, 30 Jun 2020 01:46:41: 5000000 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, 30 Jun 2020 01:46:46: 6000000 INFO @ Tue, 30 Jun 2020 01:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.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 @ Tue, 30 Jun 2020 01:46:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:46:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:46:51: 7000000 INFO @ Tue, 30 Jun 2020 01:46:52: 1000000 INFO @ Tue, 30 Jun 2020 01:46:56: 8000000 INFO @ Tue, 30 Jun 2020 01:46:57: 2000000 INFO @ Tue, 30 Jun 2020 01:47:01: 9000000 INFO @ Tue, 30 Jun 2020 01:47:03: 3000000 INFO @ Tue, 30 Jun 2020 01:47:06: 10000000 INFO @ Tue, 30 Jun 2020 01:47:09: 4000000 INFO @ Tue, 30 Jun 2020 01:47:11: 11000000 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, 30 Jun 2020 01:47:14: 5000000 INFO @ Tue, 30 Jun 2020 01:47:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.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 @ Tue, 30 Jun 2020 01:47:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:47:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:47:16: 12000000 INFO @ Tue, 30 Jun 2020 01:47:20: 6000000 INFO @ Tue, 30 Jun 2020 01:47:21: 1000000 INFO @ Tue, 30 Jun 2020 01:47:22: 13000000 INFO @ Tue, 30 Jun 2020 01:47:26: 7000000 INFO @ Tue, 30 Jun 2020 01:47:26: 2000000 INFO @ Tue, 30 Jun 2020 01:47:27: 14000000 INFO @ Tue, 30 Jun 2020 01:47:31: 8000000 INFO @ Tue, 30 Jun 2020 01:47:32: 3000000 INFO @ Tue, 30 Jun 2020 01:47:33: 15000000 INFO @ Tue, 30 Jun 2020 01:47:37: 9000000 INFO @ Tue, 30 Jun 2020 01:47:37: 4000000 INFO @ Tue, 30 Jun 2020 01:47:38: 16000000 INFO @ Tue, 30 Jun 2020 01:47:39: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:47:39: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:47:39: #1 total tags in treatment: 16192252 INFO @ Tue, 30 Jun 2020 01:47:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:47:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:47:40: #1 tags after filtering in treatment: 16192249 INFO @ Tue, 30 Jun 2020 01:47:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:47:40: #1 finished! INFO @ Tue, 30 Jun 2020 01:47:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:47:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:47:41: #2 number of paired peaks: 392 WARNING @ Tue, 30 Jun 2020 01:47:41: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Tue, 30 Jun 2020 01:47:41: start model_add_line... INFO @ Tue, 30 Jun 2020 01:47:41: start X-correlation... INFO @ Tue, 30 Jun 2020 01:47:41: end of X-cor INFO @ Tue, 30 Jun 2020 01:47:41: #2 finished! INFO @ Tue, 30 Jun 2020 01:47:41: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 01:47:41: #2 alternative fragment length(s) may be 4,42 bps INFO @ Tue, 30 Jun 2020 01:47:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.05_model.r WARNING @ Tue, 30 Jun 2020 01:47:41: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:47:41: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Tue, 30 Jun 2020 01:47:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:47:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:47:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:47:42: 10000000 INFO @ Tue, 30 Jun 2020 01:47:42: 5000000 INFO @ Tue, 30 Jun 2020 01:47:48: 6000000 INFO @ Tue, 30 Jun 2020 01:47:48: 11000000 INFO @ Tue, 30 Jun 2020 01:47:53: 7000000 INFO @ Tue, 30 Jun 2020 01:47:54: 12000000 INFO @ Tue, 30 Jun 2020 01:47:58: 8000000 INFO @ Tue, 30 Jun 2020 01:48:00: 13000000 INFO @ Tue, 30 Jun 2020 01:48:04: 9000000 INFO @ Tue, 30 Jun 2020 01:48:06: 14000000 INFO @ Tue, 30 Jun 2020 01:48:09: 10000000 INFO @ Tue, 30 Jun 2020 01:48:11: 15000000 INFO @ Tue, 30 Jun 2020 01:48:15: 11000000 INFO @ Tue, 30 Jun 2020 01:48:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:48:17: 16000000 INFO @ Tue, 30 Jun 2020 01:48:19: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:48:19: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:48:19: #1 total tags in treatment: 16192252 INFO @ Tue, 30 Jun 2020 01:48:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:48:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:48:19: #1 tags after filtering in treatment: 16192249 INFO @ Tue, 30 Jun 2020 01:48:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:48:19: #1 finished! INFO @ Tue, 30 Jun 2020 01:48:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:48:20: 12000000 INFO @ Tue, 30 Jun 2020 01:48:20: #2 number of paired peaks: 392 WARNING @ Tue, 30 Jun 2020 01:48:20: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:20: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:21: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:21: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:21: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:21: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 01:48:21: #2 alternative fragment length(s) may be 4,42 bps INFO @ Tue, 30 Jun 2020 01:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.10_model.r WARNING @ Tue, 30 Jun 2020 01:48:21: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:48:21: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Tue, 30 Jun 2020 01:48:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:48:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:48:25: 13000000 INFO @ Tue, 30 Jun 2020 01:48:31: 14000000 INFO @ Tue, 30 Jun 2020 01:48:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:48:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:48:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.05_summits.bed INFO @ Tue, 30 Jun 2020 01:48:33: Done! pass1 - making usageList (671 chroms): 1 millis pass2 - checking and writing primary data (3225 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:48:36: 15000000 INFO @ Tue, 30 Jun 2020 01:48:41: 16000000 INFO @ Tue, 30 Jun 2020 01:48:42: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 01:48:42: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 01:48:42: #1 total tags in treatment: 16192252 INFO @ Tue, 30 Jun 2020 01:48:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:48:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:48:43: #1 tags after filtering in treatment: 16192249 INFO @ Tue, 30 Jun 2020 01:48:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:48:43: #1 finished! INFO @ Tue, 30 Jun 2020 01:48:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:48:44: #2 number of paired peaks: 392 WARNING @ Tue, 30 Jun 2020 01:48:44: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:44: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:44: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:44: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:44: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:44: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 01:48:44: #2 alternative fragment length(s) may be 4,42 bps INFO @ Tue, 30 Jun 2020 01:48:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.20_model.r WARNING @ Tue, 30 Jun 2020 01:48:44: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:48:44: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Tue, 30 Jun 2020 01:48:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:48:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:48:54: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:49:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:49:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:49:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.10_summits.bed INFO @ Tue, 30 Jun 2020 01:49:12: Done! pass1 - making usageList (557 chroms): 1 millis pass2 - checking and writing primary data (2167 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:49:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:49:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:49:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:49:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX066250/SRX066250.20_summits.bed INFO @ Tue, 30 Jun 2020 01:49:37: Done! pass1 - making usageList (225 chroms): 1 millis pass2 - checking and writing primary data (433 records, 4 fields): 9 millis CompletedMACS2peakCalling