Job ID = 6529984 SRX = SRX5717045 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: 00:06:47 27086615 reads; of these: 27086615 (100.00%) were unpaired; of these: 2155542 (7.96%) aligned 0 times 19489160 (71.95%) aligned exactly 1 time 5441913 (20.09%) aligned >1 times 92.04% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 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] 7591039 / 24931073 = 0.3045 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 03:07:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.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 03:07:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:07:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:07:07: 1000000 INFO @ Tue, 30 Jun 2020 03:07:13: 2000000 INFO @ Tue, 30 Jun 2020 03:07:19: 3000000 INFO @ Tue, 30 Jun 2020 03:07:25: 4000000 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 03:07:31: 5000000 INFO @ Tue, 30 Jun 2020 03:07:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.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 03:07:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:07:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:07:36: 6000000 INFO @ Tue, 30 Jun 2020 03:07:37: 1000000 INFO @ Tue, 30 Jun 2020 03:07:42: 2000000 INFO @ Tue, 30 Jun 2020 03:07:42: 7000000 INFO @ Tue, 30 Jun 2020 03:07:47: 3000000 INFO @ Tue, 30 Jun 2020 03:07:48: 8000000 INFO @ Tue, 30 Jun 2020 03:07:52: 4000000 INFO @ Tue, 30 Jun 2020 03:07:54: 9000000 INFO @ Tue, 30 Jun 2020 03:07:58: 5000000 INFO @ Tue, 30 Jun 2020 03:07:59: 10000000 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 03:08:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.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 03:08:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:08:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:08:03: 6000000 INFO @ Tue, 30 Jun 2020 03:08:05: 11000000 INFO @ Tue, 30 Jun 2020 03:08:08: 1000000 INFO @ Tue, 30 Jun 2020 03:08:08: 7000000 INFO @ Tue, 30 Jun 2020 03:08:11: 12000000 INFO @ Tue, 30 Jun 2020 03:08:13: 8000000 INFO @ Tue, 30 Jun 2020 03:08:14: 2000000 INFO @ Tue, 30 Jun 2020 03:08:17: 13000000 INFO @ Tue, 30 Jun 2020 03:08:18: 9000000 INFO @ Tue, 30 Jun 2020 03:08:20: 3000000 INFO @ Tue, 30 Jun 2020 03:08:23: 14000000 INFO @ Tue, 30 Jun 2020 03:08:23: 10000000 INFO @ Tue, 30 Jun 2020 03:08:26: 4000000 INFO @ Tue, 30 Jun 2020 03:08:29: 11000000 INFO @ Tue, 30 Jun 2020 03:08:29: 15000000 INFO @ Tue, 30 Jun 2020 03:08:32: 5000000 INFO @ Tue, 30 Jun 2020 03:08:34: 12000000 INFO @ Tue, 30 Jun 2020 03:08:35: 16000000 INFO @ Tue, 30 Jun 2020 03:08:38: 6000000 INFO @ Tue, 30 Jun 2020 03:08:39: 13000000 INFO @ Tue, 30 Jun 2020 03:08:41: 17000000 INFO @ Tue, 30 Jun 2020 03:08:44: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:08:44: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:08:44: #1 total tags in treatment: 17340034 INFO @ Tue, 30 Jun 2020 03:08:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:08:44: #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 03:08:44: 7000000 INFO @ Tue, 30 Jun 2020 03:08:44: 14000000 INFO @ Tue, 30 Jun 2020 03:08:44: #1 tags after filtering in treatment: 17339947 INFO @ Tue, 30 Jun 2020 03:08:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:08:44: #1 finished! INFO @ Tue, 30 Jun 2020 03:08:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:08:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:08:45: #2 number of paired peaks: 102 WARNING @ Tue, 30 Jun 2020 03:08:45: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 30 Jun 2020 03:08:45: start model_add_line... INFO @ Tue, 30 Jun 2020 03:08:45: start X-correlation... INFO @ Tue, 30 Jun 2020 03:08:45: end of X-cor INFO @ Tue, 30 Jun 2020 03:08:45: #2 finished! INFO @ Tue, 30 Jun 2020 03:08:45: #2 predicted fragment length is 61 bps INFO @ Tue, 30 Jun 2020 03:08:45: #2 alternative fragment length(s) may be 41,61,82,87,107,174,192,230,301,371,445,462,512,533,576,589 bps INFO @ Tue, 30 Jun 2020 03:08:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.05_model.r WARNING @ Tue, 30 Jun 2020 03:08:45: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:08:45: #2 You may need to consider one of the other alternative d(s): 41,61,82,87,107,174,192,230,301,371,445,462,512,533,576,589 WARNING @ Tue, 30 Jun 2020 03:08:45: #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 03:08:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:08:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:08:50: 15000000 INFO @ Tue, 30 Jun 2020 03:08:50: 8000000 INFO @ Tue, 30 Jun 2020 03:08:55: 16000000 INFO @ Tue, 30 Jun 2020 03:08:55: 9000000 INFO @ Tue, 30 Jun 2020 03:09:00: 17000000 INFO @ Tue, 30 Jun 2020 03:09:01: 10000000 INFO @ Tue, 30 Jun 2020 03:09:02: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:09:02: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:09:02: #1 total tags in treatment: 17340034 INFO @ Tue, 30 Jun 2020 03:09:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:09:02: #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 03:09:03: #1 tags after filtering in treatment: 17339947 INFO @ Tue, 30 Jun 2020 03:09:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:09:03: #1 finished! INFO @ Tue, 30 Jun 2020 03:09:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:09:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:09:04: #2 number of paired peaks: 102 WARNING @ Tue, 30 Jun 2020 03:09:04: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 30 Jun 2020 03:09:04: start model_add_line... INFO @ Tue, 30 Jun 2020 03:09:04: start X-correlation... INFO @ Tue, 30 Jun 2020 03:09:04: end of X-cor INFO @ Tue, 30 Jun 2020 03:09:04: #2 finished! INFO @ Tue, 30 Jun 2020 03:09:04: #2 predicted fragment length is 61 bps INFO @ Tue, 30 Jun 2020 03:09:04: #2 alternative fragment length(s) may be 41,61,82,87,107,174,192,230,301,371,445,462,512,533,576,589 bps INFO @ Tue, 30 Jun 2020 03:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.10_model.r WARNING @ Tue, 30 Jun 2020 03:09:04: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:09:04: #2 You may need to consider one of the other alternative d(s): 41,61,82,87,107,174,192,230,301,371,445,462,512,533,576,589 WARNING @ Tue, 30 Jun 2020 03:09:04: #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 03:09:04: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:09:07: 11000000 INFO @ Tue, 30 Jun 2020 03:09:12: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:09:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:09:18: 13000000 INFO @ Tue, 30 Jun 2020 03:09:24: 14000000 INFO @ Tue, 30 Jun 2020 03:09:30: 15000000 INFO @ Tue, 30 Jun 2020 03:09:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:09:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:09:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.05_summits.bed INFO @ Tue, 30 Jun 2020 03:09:33: Done! pass1 - making usageList (274 chroms): 1 millis pass2 - checking and writing primary data (1014 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:09:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:09:36: 16000000 INFO @ Tue, 30 Jun 2020 03:09:42: 17000000 INFO @ Tue, 30 Jun 2020 03:09:44: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:09:44: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:09:44: #1 total tags in treatment: 17340034 INFO @ Tue, 30 Jun 2020 03:09:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:09:44: #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 03:09:45: #1 tags after filtering in treatment: 17339947 INFO @ Tue, 30 Jun 2020 03:09:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:09:45: #1 finished! INFO @ Tue, 30 Jun 2020 03:09:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:09:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:09:46: #2 number of paired peaks: 102 WARNING @ Tue, 30 Jun 2020 03:09:46: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 30 Jun 2020 03:09:46: start model_add_line... INFO @ Tue, 30 Jun 2020 03:09:46: start X-correlation... INFO @ Tue, 30 Jun 2020 03:09:46: end of X-cor INFO @ Tue, 30 Jun 2020 03:09:46: #2 finished! INFO @ Tue, 30 Jun 2020 03:09:46: #2 predicted fragment length is 61 bps INFO @ Tue, 30 Jun 2020 03:09:46: #2 alternative fragment length(s) may be 41,61,82,87,107,174,192,230,301,371,445,462,512,533,576,589 bps INFO @ Tue, 30 Jun 2020 03:09:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.20_model.r WARNING @ Tue, 30 Jun 2020 03:09:46: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:09:46: #2 You may need to consider one of the other alternative d(s): 41,61,82,87,107,174,192,230,301,371,445,462,512,533,576,589 WARNING @ Tue, 30 Jun 2020 03:09:46: #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 03:09:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:09:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:09:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:09:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:09:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.10_summits.bed INFO @ Tue, 30 Jun 2020 03:09:51: Done! pass1 - making usageList (124 chroms): 0 millis pass2 - checking and writing primary data (353 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:10:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:10:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:10:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:10:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717045/SRX5717045.20_summits.bed INFO @ Tue, 30 Jun 2020 03:10:36: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (92 records, 4 fields): 4 millis CompletedMACS2peakCalling