Job ID = 6529551 SRX = SRX3159469 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:35 22405921 reads; of these: 22405921 (100.00%) were unpaired; of these: 1058013 (4.72%) aligned 0 times 17010624 (75.92%) aligned exactly 1 time 4337284 (19.36%) aligned >1 times 95.28% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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] 3013512 / 21347908 = 0.1412 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 02:29:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.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 02:29:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:29:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:29:59: 1000000 INFO @ Tue, 30 Jun 2020 02:30:04: 2000000 INFO @ Tue, 30 Jun 2020 02:30:10: 3000000 INFO @ Tue, 30 Jun 2020 02:30:15: 4000000 INFO @ Tue, 30 Jun 2020 02:30:20: 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 02:30:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.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 02:30:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:30:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:30:25: 6000000 INFO @ Tue, 30 Jun 2020 02:30:30: 1000000 INFO @ Tue, 30 Jun 2020 02:30:31: 7000000 INFO @ Tue, 30 Jun 2020 02:30:36: 8000000 INFO @ Tue, 30 Jun 2020 02:30:37: 2000000 INFO @ Tue, 30 Jun 2020 02:30:42: 9000000 INFO @ Tue, 30 Jun 2020 02:30:44: 3000000 INFO @ Tue, 30 Jun 2020 02:30:47: 10000000 INFO @ Tue, 30 Jun 2020 02:30:51: 4000000 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 02:30:53: 11000000 INFO @ Tue, 30 Jun 2020 02:30:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.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 02:30:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:30:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:30:58: 5000000 INFO @ Tue, 30 Jun 2020 02:30:58: 12000000 INFO @ Tue, 30 Jun 2020 02:31:00: 1000000 INFO @ Tue, 30 Jun 2020 02:31:03: 13000000 INFO @ Tue, 30 Jun 2020 02:31:05: 6000000 INFO @ Tue, 30 Jun 2020 02:31:07: 2000000 INFO @ Tue, 30 Jun 2020 02:31:09: 14000000 INFO @ Tue, 30 Jun 2020 02:31:12: 7000000 INFO @ Tue, 30 Jun 2020 02:31:14: 3000000 INFO @ Tue, 30 Jun 2020 02:31:14: 15000000 INFO @ Tue, 30 Jun 2020 02:31:18: 8000000 INFO @ Tue, 30 Jun 2020 02:31:20: 16000000 INFO @ Tue, 30 Jun 2020 02:31:20: 4000000 INFO @ Tue, 30 Jun 2020 02:31:25: 9000000 INFO @ Tue, 30 Jun 2020 02:31:26: 17000000 INFO @ Tue, 30 Jun 2020 02:31:27: 5000000 INFO @ Tue, 30 Jun 2020 02:31:31: 18000000 INFO @ Tue, 30 Jun 2020 02:31:32: 10000000 INFO @ Tue, 30 Jun 2020 02:31:33: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:31:33: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:31:33: #1 total tags in treatment: 18334396 INFO @ Tue, 30 Jun 2020 02:31:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:31:33: #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 02:31:34: 6000000 INFO @ Tue, 30 Jun 2020 02:31:34: #1 tags after filtering in treatment: 18334395 INFO @ Tue, 30 Jun 2020 02:31:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:31:34: #1 finished! INFO @ Tue, 30 Jun 2020 02:31:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:31:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:31:35: #2 number of paired peaks: 181 WARNING @ Tue, 30 Jun 2020 02:31:35: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 30 Jun 2020 02:31:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:31:36: start X-correlation... INFO @ Tue, 30 Jun 2020 02:31:36: end of X-cor INFO @ Tue, 30 Jun 2020 02:31:36: #2 finished! INFO @ Tue, 30 Jun 2020 02:31:36: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 02:31:36: #2 alternative fragment length(s) may be 4,54 bps INFO @ Tue, 30 Jun 2020 02:31:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.05_model.r WARNING @ Tue, 30 Jun 2020 02:31:36: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:31:36: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Tue, 30 Jun 2020 02:31:36: #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 02:31:36: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:31:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:31:39: 11000000 INFO @ Tue, 30 Jun 2020 02:31:40: 7000000 INFO @ Tue, 30 Jun 2020 02:31:45: 12000000 INFO @ Tue, 30 Jun 2020 02:31:47: 8000000 INFO @ Tue, 30 Jun 2020 02:31:51: 13000000 INFO @ Tue, 30 Jun 2020 02:31:54: 9000000 INFO @ Tue, 30 Jun 2020 02:31:58: 14000000 INFO @ Tue, 30 Jun 2020 02:32:00: 10000000 INFO @ Tue, 30 Jun 2020 02:32:04: 15000000 INFO @ Tue, 30 Jun 2020 02:32:07: 11000000 INFO @ Tue, 30 Jun 2020 02:32:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:32:12: 16000000 INFO @ Tue, 30 Jun 2020 02:32:14: 12000000 INFO @ Tue, 30 Jun 2020 02:32:18: 17000000 INFO @ Tue, 30 Jun 2020 02:32:20: 13000000 INFO @ Tue, 30 Jun 2020 02:32:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:32:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:32:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.05_summits.bed INFO @ Tue, 30 Jun 2020 02:32:25: Done! pass1 - making usageList (431 chroms): 2 millis pass2 - checking and writing primary data (3685 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:32:25: 18000000 INFO @ Tue, 30 Jun 2020 02:32:27: 14000000 INFO @ Tue, 30 Jun 2020 02:32:28: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:32:28: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:32:28: #1 total tags in treatment: 18334396 INFO @ Tue, 30 Jun 2020 02:32:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:28: #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 02:32:29: #1 tags after filtering in treatment: 18334395 INFO @ Tue, 30 Jun 2020 02:32:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:29: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:32:30: #2 number of paired peaks: 181 WARNING @ Tue, 30 Jun 2020 02:32:30: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 30 Jun 2020 02:32:30: start model_add_line... INFO @ Tue, 30 Jun 2020 02:32:30: start X-correlation... INFO @ Tue, 30 Jun 2020 02:32:30: end of X-cor INFO @ Tue, 30 Jun 2020 02:32:30: #2 finished! INFO @ Tue, 30 Jun 2020 02:32:30: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 02:32:30: #2 alternative fragment length(s) may be 4,54 bps INFO @ Tue, 30 Jun 2020 02:32:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.10_model.r WARNING @ Tue, 30 Jun 2020 02:32:30: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:32:30: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Tue, 30 Jun 2020 02:32:30: #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 02:32:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:32:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:32:33: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:32:40: 16000000 INFO @ Tue, 30 Jun 2020 02:32:46: 17000000 INFO @ Tue, 30 Jun 2020 02:32:52: 18000000 INFO @ Tue, 30 Jun 2020 02:32:55: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:32:55: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:32:55: #1 total tags in treatment: 18334396 INFO @ Tue, 30 Jun 2020 02:32:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:55: #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 02:32:56: #1 tags after filtering in treatment: 18334395 INFO @ Tue, 30 Jun 2020 02:32:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:32:57: #2 number of paired peaks: 181 WARNING @ Tue, 30 Jun 2020 02:32:57: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 30 Jun 2020 02:32:57: start model_add_line... INFO @ Tue, 30 Jun 2020 02:32:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:32:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:32:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:32:57: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 02:32:57: #2 alternative fragment length(s) may be 4,54 bps INFO @ Tue, 30 Jun 2020 02:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.20_model.r WARNING @ Tue, 30 Jun 2020 02:32:57: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:32:57: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Tue, 30 Jun 2020 02:32:57: #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 02:32:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:33:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:33:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.10_summits.bed INFO @ Tue, 30 Jun 2020 02:33:20: Done! pass1 - making usageList (255 chroms): 2 millis pass2 - checking and writing primary data (1111 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:33:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:33:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159469/SRX3159469.20_summits.bed INFO @ Tue, 30 Jun 2020 02:33:47: Done! pass1 - making usageList (112 chroms): 1 millis pass2 - checking and writing primary data (285 records, 4 fields): 8 millis CompletedMACS2peakCalling