Job ID = 6530047 SRX = SRX647919 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: 00:04:31 16412362 reads; of these: 16412362 (100.00%) were unpaired; of these: 705230 (4.30%) aligned 0 times 12642056 (77.03%) aligned exactly 1 time 3065076 (18.68%) aligned >1 times 95.70% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 2202101 / 15707132 = 0.1402 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 03:24:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.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 03:24:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:24:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:24:59: 1000000 INFO @ Tue, 30 Jun 2020 03:25:05: 2000000 INFO @ Tue, 30 Jun 2020 03:25:11: 3000000 INFO @ Tue, 30 Jun 2020 03:25:18: 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 03:25:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.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 03:25:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:25:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:25:25: 5000000 INFO @ Tue, 30 Jun 2020 03:25:29: 1000000 INFO @ Tue, 30 Jun 2020 03:25:32: 6000000 INFO @ Tue, 30 Jun 2020 03:25:36: 2000000 INFO @ Tue, 30 Jun 2020 03:25:39: 7000000 INFO @ Tue, 30 Jun 2020 03:25:44: 3000000 INFO @ Tue, 30 Jun 2020 03:25:47: 8000000 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 03:25:51: 4000000 INFO @ Tue, 30 Jun 2020 03:25:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.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 03:25:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:25:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:25:54: 9000000 INFO @ Tue, 30 Jun 2020 03:25:58: 5000000 INFO @ Tue, 30 Jun 2020 03:26:00: 1000000 INFO @ Tue, 30 Jun 2020 03:26:01: 10000000 INFO @ Tue, 30 Jun 2020 03:26:05: 6000000 INFO @ Tue, 30 Jun 2020 03:26:07: 2000000 INFO @ Tue, 30 Jun 2020 03:26:09: 11000000 INFO @ Tue, 30 Jun 2020 03:26:13: 7000000 INFO @ Tue, 30 Jun 2020 03:26:15: 3000000 INFO @ Tue, 30 Jun 2020 03:26:17: 12000000 INFO @ Tue, 30 Jun 2020 03:26:20: 8000000 INFO @ Tue, 30 Jun 2020 03:26:23: 4000000 INFO @ Tue, 30 Jun 2020 03:26:25: 13000000 INFO @ Tue, 30 Jun 2020 03:26:27: 9000000 INFO @ Tue, 30 Jun 2020 03:26:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:26:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:26:29: #1 total tags in treatment: 13505031 INFO @ Tue, 30 Jun 2020 03:26:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:26:29: #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 03:26:30: #1 tags after filtering in treatment: 13505029 INFO @ Tue, 30 Jun 2020 03:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:26:30: #1 finished! INFO @ Tue, 30 Jun 2020 03:26:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:26:30: 5000000 INFO @ Tue, 30 Jun 2020 03:26:31: #2 number of paired peaks: 210 WARNING @ Tue, 30 Jun 2020 03:26:31: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 30 Jun 2020 03:26:31: start model_add_line... INFO @ Tue, 30 Jun 2020 03:26:31: start X-correlation... INFO @ Tue, 30 Jun 2020 03:26:31: end of X-cor INFO @ Tue, 30 Jun 2020 03:26:31: #2 finished! INFO @ Tue, 30 Jun 2020 03:26:31: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 03:26:31: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 30 Jun 2020 03:26:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.05_model.r WARNING @ Tue, 30 Jun 2020 03:26:31: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:26:31: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 30 Jun 2020 03:26:31: #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 03:26:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:26:34: 10000000 INFO @ Tue, 30 Jun 2020 03:26:38: 6000000 INFO @ Tue, 30 Jun 2020 03:26:42: 11000000 INFO @ Tue, 30 Jun 2020 03:26:45: 7000000 INFO @ Tue, 30 Jun 2020 03:26:49: 12000000 INFO @ Tue, 30 Jun 2020 03:26:52: 8000000 INFO @ Tue, 30 Jun 2020 03:26:57: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:26:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:26:59: 9000000 INFO @ Tue, 30 Jun 2020 03:27:00: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:27:00: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:27:00: #1 total tags in treatment: 13505031 INFO @ Tue, 30 Jun 2020 03:27:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:27:00: #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 03:27:01: #1 tags after filtering in treatment: 13505029 INFO @ Tue, 30 Jun 2020 03:27:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:27:01: #1 finished! INFO @ Tue, 30 Jun 2020 03:27:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:27:02: #2 number of paired peaks: 210 WARNING @ Tue, 30 Jun 2020 03:27:02: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 30 Jun 2020 03:27:02: start model_add_line... INFO @ Tue, 30 Jun 2020 03:27:02: start X-correlation... INFO @ Tue, 30 Jun 2020 03:27:02: end of X-cor INFO @ Tue, 30 Jun 2020 03:27:02: #2 finished! INFO @ Tue, 30 Jun 2020 03:27:02: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 03:27:02: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 30 Jun 2020 03:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.10_model.r WARNING @ Tue, 30 Jun 2020 03:27:02: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:27:02: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 30 Jun 2020 03:27:02: #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 03:27:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:27:06: 10000000 INFO @ Tue, 30 Jun 2020 03:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:27:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:27:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.05_summits.bed INFO @ Tue, 30 Jun 2020 03:27:12: Done! pass1 - making usageList (434 chroms): 1 millis pass2 - checking and writing primary data (1491 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:27:12: 11000000 INFO @ Tue, 30 Jun 2020 03:27:19: 12000000 INFO @ Tue, 30 Jun 2020 03:27:26: 13000000 INFO @ Tue, 30 Jun 2020 03:27:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:27:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:27:29: #1 total tags in treatment: 13505031 INFO @ Tue, 30 Jun 2020 03:27:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:27:29: #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 03:27:30: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:27:30: #1 tags after filtering in treatment: 13505029 INFO @ Tue, 30 Jun 2020 03:27:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:27:30: #1 finished! INFO @ Tue, 30 Jun 2020 03:27:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:27:30: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:27:31: #2 number of paired peaks: 210 WARNING @ Tue, 30 Jun 2020 03:27:31: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 30 Jun 2020 03:27:31: start model_add_line... INFO @ Tue, 30 Jun 2020 03:27:31: start X-correlation... INFO @ Tue, 30 Jun 2020 03:27:31: end of X-cor INFO @ Tue, 30 Jun 2020 03:27:31: #2 finished! INFO @ Tue, 30 Jun 2020 03:27:31: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 03:27:31: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 30 Jun 2020 03:27:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.20_model.r WARNING @ Tue, 30 Jun 2020 03:27:31: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:27:31: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 30 Jun 2020 03:27:31: #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 03:27:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:27:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:27:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:27:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:27:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.10_summits.bed INFO @ Tue, 30 Jun 2020 03:27:43: Done! pass1 - making usageList (264 chroms): 1 millis pass2 - checking and writing primary data (611 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:27:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:28:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:28:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:28:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX647919/SRX647919.20_summits.bed INFO @ Tue, 30 Jun 2020 03:28:11: Done! pass1 - making usageList (118 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 6 millis CompletedMACS2peakCalling