Job ID = 6529789 SRX = SRX4828017 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: 00:03:52 15880701 reads; of these: 15880701 (100.00%) were unpaired; of these: 1269758 (8.00%) aligned 0 times 11581302 (72.93%) aligned exactly 1 time 3029641 (19.08%) aligned >1 times 92.00% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 2656932 / 14610943 = 0.1818 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 02:46:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.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 02:46:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:26: 1000000 INFO @ Tue, 30 Jun 2020 02:46:31: 2000000 INFO @ Tue, 30 Jun 2020 02:46:36: 3000000 INFO @ Tue, 30 Jun 2020 02:46:42: 4000000 INFO @ Tue, 30 Jun 2020 02:46:47: 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 02:46:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.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 02:46:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:52: 6000000 INFO @ Tue, 30 Jun 2020 02:46:57: 1000000 INFO @ Tue, 30 Jun 2020 02:46:57: 7000000 INFO @ Tue, 30 Jun 2020 02:47:02: 2000000 INFO @ Tue, 30 Jun 2020 02:47:03: 8000000 INFO @ Tue, 30 Jun 2020 02:47:08: 3000000 INFO @ Tue, 30 Jun 2020 02:47:08: 9000000 INFO @ Tue, 30 Jun 2020 02:47:13: 4000000 INFO @ Tue, 30 Jun 2020 02:47:14: 10000000 INFO @ Tue, 30 Jun 2020 02:47:19: 5000000 INFO @ Tue, 30 Jun 2020 02:47:19: 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 02:47:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.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 02:47:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:24: 6000000 INFO @ Tue, 30 Jun 2020 02:47:25: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:47:25: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:47:25: #1 total tags in treatment: 11954011 INFO @ Tue, 30 Jun 2020 02:47:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:47:25: #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 02:47:25: #1 tags after filtering in treatment: 11953903 INFO @ Tue, 30 Jun 2020 02:47:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:47:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:47:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:47:26: #2 number of paired peaks: 318 WARNING @ Tue, 30 Jun 2020 02:47:26: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 30 Jun 2020 02:47:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:47:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:47:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:47:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:47:26: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 02:47:26: #2 alternative fragment length(s) may be 3,55,558 bps INFO @ Tue, 30 Jun 2020 02:47:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.05_model.r WARNING @ Tue, 30 Jun 2020 02:47:26: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:47:26: #2 You may need to consider one of the other alternative d(s): 3,55,558 WARNING @ Tue, 30 Jun 2020 02:47:26: #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 02:47:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:47:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:47:27: 1000000 INFO @ Tue, 30 Jun 2020 02:47:30: 7000000 INFO @ Tue, 30 Jun 2020 02:47:32: 2000000 INFO @ Tue, 30 Jun 2020 02:47:35: 8000000 INFO @ Tue, 30 Jun 2020 02:47:38: 3000000 INFO @ Tue, 30 Jun 2020 02:47:40: 9000000 INFO @ Tue, 30 Jun 2020 02:47:43: 4000000 INFO @ Tue, 30 Jun 2020 02:47:46: 10000000 INFO @ Tue, 30 Jun 2020 02:47:49: 5000000 INFO @ Tue, 30 Jun 2020 02:47:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:47:52: 11000000 INFO @ Tue, 30 Jun 2020 02:47:54: 6000000 INFO @ Tue, 30 Jun 2020 02:47:57: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:47:57: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:47:57: #1 total tags in treatment: 11954011 INFO @ Tue, 30 Jun 2020 02:47:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:47:57: #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 02:47:58: #1 tags after filtering in treatment: 11953903 INFO @ Tue, 30 Jun 2020 02:47:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:47:58: #1 finished! INFO @ Tue, 30 Jun 2020 02:47:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:47:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:47:58: #2 number of paired peaks: 318 WARNING @ Tue, 30 Jun 2020 02:47:58: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 30 Jun 2020 02:47:58: start model_add_line... INFO @ Tue, 30 Jun 2020 02:47:58: start X-correlation... INFO @ Tue, 30 Jun 2020 02:47:58: end of X-cor INFO @ Tue, 30 Jun 2020 02:47:58: #2 finished! INFO @ Tue, 30 Jun 2020 02:47:58: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 02:47:58: #2 alternative fragment length(s) may be 3,55,558 bps INFO @ Tue, 30 Jun 2020 02:47:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.10_model.r WARNING @ Tue, 30 Jun 2020 02:47:58: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:47:58: #2 You may need to consider one of the other alternative d(s): 3,55,558 WARNING @ Tue, 30 Jun 2020 02:47:58: #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 02:47:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:47:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:47:59: 7000000 INFO @ Tue, 30 Jun 2020 02:48:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:48:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:48:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.05_summits.bed INFO @ Tue, 30 Jun 2020 02:48:02: Done! pass1 - making usageList (394 chroms): 1 millis pass2 - checking and writing primary data (1121 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:48:05: 8000000 INFO @ Tue, 30 Jun 2020 02:48:10: 9000000 INFO @ Tue, 30 Jun 2020 02:48:15: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:48:20: 11000000 INFO @ Tue, 30 Jun 2020 02:48:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:48:25: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:48:25: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:48:25: #1 total tags in treatment: 11954011 INFO @ Tue, 30 Jun 2020 02:48:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:25: #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 02:48:26: #1 tags after filtering in treatment: 11953903 INFO @ Tue, 30 Jun 2020 02:48:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:26: #2 number of paired peaks: 318 WARNING @ Tue, 30 Jun 2020 02:48:26: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:26: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 02:48:26: #2 alternative fragment length(s) may be 3,55,558 bps INFO @ Tue, 30 Jun 2020 02:48:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.20_model.r WARNING @ Tue, 30 Jun 2020 02:48:26: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:48:26: #2 You may need to consider one of the other alternative d(s): 3,55,558 WARNING @ Tue, 30 Jun 2020 02:48:26: #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 02:48:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:48:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:48:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.10_summits.bed INFO @ Tue, 30 Jun 2020 02:48:33: Done! pass1 - making usageList (198 chroms): 1 millis pass2 - checking and writing primary data (467 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:48:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828017/SRX4828017.20_summits.bed INFO @ Tue, 30 Jun 2020 02:49:01: Done! pass1 - making usageList (92 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 3 millis CompletedMACS2peakCalling