Job ID = 6529598 SRX = SRX335507 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: 00:06:02 28429556 reads; of these: 28429556 (100.00%) were unpaired; of these: 10380863 (36.51%) aligned 0 times 14128883 (49.70%) aligned exactly 1 time 3919810 (13.79%) aligned >1 times 63.49% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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] 4312107 / 18048693 = 0.2389 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 02:41:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.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 02:41:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:41:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:41:09: 1000000 INFO @ Tue, 30 Jun 2020 02:41:18: 2000000 INFO @ Tue, 30 Jun 2020 02:41:26: 3000000 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 02:41:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.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 02:41:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:41:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:41:34: 4000000 INFO @ Tue, 30 Jun 2020 02:41:39: 1000000 INFO @ Tue, 30 Jun 2020 02:41:44: 5000000 INFO @ Tue, 30 Jun 2020 02:41:47: 2000000 INFO @ Tue, 30 Jun 2020 02:41:52: 6000000 INFO @ Tue, 30 Jun 2020 02:41:55: 3000000 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 02:42:00: 7000000 INFO @ Tue, 30 Jun 2020 02:42:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.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 02:42:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:42:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:42:03: 4000000 INFO @ Tue, 30 Jun 2020 02:42:09: 8000000 INFO @ Tue, 30 Jun 2020 02:42:09: 1000000 INFO @ Tue, 30 Jun 2020 02:42:12: 5000000 INFO @ Tue, 30 Jun 2020 02:42:18: 9000000 INFO @ Tue, 30 Jun 2020 02:42:18: 2000000 INFO @ Tue, 30 Jun 2020 02:42:20: 6000000 INFO @ Tue, 30 Jun 2020 02:42:26: 10000000 INFO @ Tue, 30 Jun 2020 02:42:26: 3000000 INFO @ Tue, 30 Jun 2020 02:42:29: 7000000 INFO @ Tue, 30 Jun 2020 02:42:34: 11000000 INFO @ Tue, 30 Jun 2020 02:42:35: 4000000 INFO @ Tue, 30 Jun 2020 02:42:37: 8000000 INFO @ Tue, 30 Jun 2020 02:42:43: 5000000 INFO @ Tue, 30 Jun 2020 02:42:44: 12000000 INFO @ Tue, 30 Jun 2020 02:42:45: 9000000 INFO @ Tue, 30 Jun 2020 02:42:51: 6000000 INFO @ Tue, 30 Jun 2020 02:42:52: 13000000 INFO @ Tue, 30 Jun 2020 02:42:54: 10000000 INFO @ Tue, 30 Jun 2020 02:42:59: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:42:59: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:42:59: #1 total tags in treatment: 13736586 INFO @ Tue, 30 Jun 2020 02:42:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:42:59: #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 02:43:00: 7000000 INFO @ Tue, 30 Jun 2020 02:43:00: #1 tags after filtering in treatment: 13736586 INFO @ Tue, 30 Jun 2020 02:43:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:43:00: #1 finished! INFO @ Tue, 30 Jun 2020 02:43:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:43:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:43:01: #2 number of paired peaks: 110 WARNING @ Tue, 30 Jun 2020 02:43:01: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 30 Jun 2020 02:43:01: start model_add_line... INFO @ Tue, 30 Jun 2020 02:43:01: start X-correlation... INFO @ Tue, 30 Jun 2020 02:43:01: end of X-cor INFO @ Tue, 30 Jun 2020 02:43:01: #2 finished! INFO @ Tue, 30 Jun 2020 02:43:01: #2 predicted fragment length is 56 bps INFO @ Tue, 30 Jun 2020 02:43:01: #2 alternative fragment length(s) may be 3,13,17,30,56,414,438,489,533,557,580 bps INFO @ Tue, 30 Jun 2020 02:43:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.05_model.r WARNING @ Tue, 30 Jun 2020 02:43:01: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:43:01: #2 You may need to consider one of the other alternative d(s): 3,13,17,30,56,414,438,489,533,557,580 WARNING @ Tue, 30 Jun 2020 02:43:01: #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 02:43:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:43:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:43:02: 11000000 INFO @ Tue, 30 Jun 2020 02:43:08: 8000000 INFO @ Tue, 30 Jun 2020 02:43:11: 12000000 INFO @ Tue, 30 Jun 2020 02:43:16: 9000000 INFO @ Tue, 30 Jun 2020 02:43:19: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:43:24: 10000000 INFO @ Tue, 30 Jun 2020 02:43:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:43:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:43:25: #1 total tags in treatment: 13736586 INFO @ Tue, 30 Jun 2020 02:43:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:43:25: #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 02:43:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:43:26: #1 tags after filtering in treatment: 13736586 INFO @ Tue, 30 Jun 2020 02:43:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:43:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:43:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:43:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:43:27: #2 number of paired peaks: 110 WARNING @ Tue, 30 Jun 2020 02:43:27: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 30 Jun 2020 02:43:27: start model_add_line... INFO @ Tue, 30 Jun 2020 02:43:27: start X-correlation... INFO @ Tue, 30 Jun 2020 02:43:27: end of X-cor INFO @ Tue, 30 Jun 2020 02:43:27: #2 finished! INFO @ Tue, 30 Jun 2020 02:43:27: #2 predicted fragment length is 56 bps INFO @ Tue, 30 Jun 2020 02:43:27: #2 alternative fragment length(s) may be 3,13,17,30,56,414,438,489,533,557,580 bps INFO @ Tue, 30 Jun 2020 02:43:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.10_model.r WARNING @ Tue, 30 Jun 2020 02:43:27: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:43:27: #2 You may need to consider one of the other alternative d(s): 3,13,17,30,56,414,438,489,533,557,580 WARNING @ Tue, 30 Jun 2020 02:43:27: #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 02:43:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:43:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:43:31: 11000000 INFO @ Tue, 30 Jun 2020 02:43:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:43:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:43:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.05_summits.bed INFO @ Tue, 30 Jun 2020 02:43:39: Done! INFO @ Tue, 30 Jun 2020 02:43:39: 12000000 pass1 - making usageList (333 chroms): 2 millis pass2 - checking and writing primary data (1134 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:43:46: 13000000 INFO @ Tue, 30 Jun 2020 02:43:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:43:51: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:43:51: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:43:51: #1 total tags in treatment: 13736586 INFO @ Tue, 30 Jun 2020 02:43:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:43:51: #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 02:43:52: #1 tags after filtering in treatment: 13736586 INFO @ Tue, 30 Jun 2020 02:43:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:43:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:43:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:43:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:43:53: #2 number of paired peaks: 110 WARNING @ Tue, 30 Jun 2020 02:43:53: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Tue, 30 Jun 2020 02:43:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:43:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:43:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:43:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:43:53: #2 predicted fragment length is 56 bps INFO @ Tue, 30 Jun 2020 02:43:53: #2 alternative fragment length(s) may be 3,13,17,30,56,414,438,489,533,557,580 bps INFO @ Tue, 30 Jun 2020 02:43:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.20_model.r WARNING @ Tue, 30 Jun 2020 02:43:53: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:43:53: #2 You may need to consider one of the other alternative d(s): 3,13,17,30,56,414,438,489,533,557,580 WARNING @ Tue, 30 Jun 2020 02:43:53: #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 02:43:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:43:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:44:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:44:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:44:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.10_summits.bed INFO @ Tue, 30 Jun 2020 02:44:04: Done! pass1 - making usageList (136 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:44:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:44:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:44:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:44:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335507/SRX335507.20_summits.bed INFO @ Tue, 30 Jun 2020 02:44:29: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 5 millis CompletedMACS2peakCalling