Job ID = 6529754 SRX = SRX4669062 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: 00:03:58 16206203 reads; of these: 16206203 (100.00%) were unpaired; of these: 826075 (5.10%) aligned 0 times 12863348 (79.37%) aligned exactly 1 time 2516780 (15.53%) aligned >1 times 94.90% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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] 2345061 / 15380128 = 0.1525 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 02:39:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.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 02:39:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:39:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:39:28: 1000000 INFO @ Tue, 30 Jun 2020 02:39:35: 2000000 INFO @ Tue, 30 Jun 2020 02:39:42: 3000000 INFO @ Tue, 30 Jun 2020 02:39:49: 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 02:39:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.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 02:39:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:39:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:39:56: 5000000 INFO @ Tue, 30 Jun 2020 02:39:58: 1000000 INFO @ Tue, 30 Jun 2020 02:40:04: 6000000 INFO @ Tue, 30 Jun 2020 02:40:05: 2000000 INFO @ Tue, 30 Jun 2020 02:40:11: 7000000 INFO @ Tue, 30 Jun 2020 02:40:12: 3000000 INFO @ Tue, 30 Jun 2020 02:40:18: 8000000 INFO @ Tue, 30 Jun 2020 02:40:19: 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 02:40:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.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 02:40:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:40:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:40:25: 9000000 INFO @ Tue, 30 Jun 2020 02:40:26: 5000000 INFO @ Tue, 30 Jun 2020 02:40:30: 1000000 INFO @ Tue, 30 Jun 2020 02:40:33: 10000000 INFO @ Tue, 30 Jun 2020 02:40:33: 6000000 INFO @ Tue, 30 Jun 2020 02:40:38: 2000000 INFO @ Tue, 30 Jun 2020 02:40:40: 7000000 INFO @ Tue, 30 Jun 2020 02:40:40: 11000000 INFO @ Tue, 30 Jun 2020 02:40:45: 3000000 INFO @ Tue, 30 Jun 2020 02:40:47: 8000000 INFO @ Tue, 30 Jun 2020 02:40:48: 12000000 INFO @ Tue, 30 Jun 2020 02:40:52: 4000000 INFO @ Tue, 30 Jun 2020 02:40:55: 9000000 INFO @ Tue, 30 Jun 2020 02:40:55: 13000000 INFO @ Tue, 30 Jun 2020 02:40:55: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:40:55: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:40:55: #1 total tags in treatment: 13035067 INFO @ Tue, 30 Jun 2020 02:40:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:40:55: #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 02:40:56: #1 tags after filtering in treatment: 13035049 INFO @ Tue, 30 Jun 2020 02:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:40:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:40:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:40:57: #2 number of paired peaks: 126 WARNING @ Tue, 30 Jun 2020 02:40:57: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 30 Jun 2020 02:40:57: start model_add_line... INFO @ Tue, 30 Jun 2020 02:40:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:40:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:40:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:40:57: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 02:40:57: #2 alternative fragment length(s) may be 3,47,533 bps INFO @ Tue, 30 Jun 2020 02:40:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.05_model.r WARNING @ Tue, 30 Jun 2020 02:40:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:40:57: #2 You may need to consider one of the other alternative d(s): 3,47,533 WARNING @ Tue, 30 Jun 2020 02:40:57: #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 02:40:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:40:59: 5000000 INFO @ Tue, 30 Jun 2020 02:41:01: 10000000 INFO @ Tue, 30 Jun 2020 02:41:05: 6000000 INFO @ Tue, 30 Jun 2020 02:41:08: 11000000 INFO @ Tue, 30 Jun 2020 02:41:12: 7000000 INFO @ Tue, 30 Jun 2020 02:41:15: 12000000 INFO @ Tue, 30 Jun 2020 02:41:18: 8000000 INFO @ Tue, 30 Jun 2020 02:41:22: 13000000 INFO @ Tue, 30 Jun 2020 02:41:22: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:41:22: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:41:22: #1 total tags in treatment: 13035067 INFO @ Tue, 30 Jun 2020 02:41:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:41:22: #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 02:41:22: #1 tags after filtering in treatment: 13035049 INFO @ Tue, 30 Jun 2020 02:41:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:41:22: #1 finished! INFO @ Tue, 30 Jun 2020 02:41:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:41:23: #2 number of paired peaks: 126 WARNING @ Tue, 30 Jun 2020 02:41:23: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 30 Jun 2020 02:41:23: start model_add_line... INFO @ Tue, 30 Jun 2020 02:41:23: start X-correlation... INFO @ Tue, 30 Jun 2020 02:41:23: end of X-cor INFO @ Tue, 30 Jun 2020 02:41:23: #2 finished! INFO @ Tue, 30 Jun 2020 02:41:23: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 02:41:23: #2 alternative fragment length(s) may be 3,47,533 bps INFO @ Tue, 30 Jun 2020 02:41:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.10_model.r WARNING @ Tue, 30 Jun 2020 02:41:23: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:41:23: #2 You may need to consider one of the other alternative d(s): 3,47,533 WARNING @ Tue, 30 Jun 2020 02:41:23: #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 02:41:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:41:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:41:24: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:41:24: 9000000 INFO @ Tue, 30 Jun 2020 02:41:30: 10000000 INFO @ Tue, 30 Jun 2020 02:41:37: 11000000 INFO @ Tue, 30 Jun 2020 02:41:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:41:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:41:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.05_summits.bed INFO @ Tue, 30 Jun 2020 02:41:37: Done! pass1 - making usageList (407 chroms): 1 millis pass2 - checking and writing primary data (1301 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:41:42: 12000000 INFO @ Tue, 30 Jun 2020 02:41:48: 13000000 INFO @ Tue, 30 Jun 2020 02:41:48: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:41:48: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:41:48: #1 total tags in treatment: 13035067 INFO @ Tue, 30 Jun 2020 02:41:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:41:48: #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 02:41:49: #1 tags after filtering in treatment: 13035049 INFO @ Tue, 30 Jun 2020 02:41:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:41:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:41:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:41:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:41:50: #2 number of paired peaks: 126 WARNING @ Tue, 30 Jun 2020 02:41:50: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 30 Jun 2020 02:41:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:41:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:41:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:41:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:41:50: #2 predicted fragment length is 47 bps INFO @ Tue, 30 Jun 2020 02:41:50: #2 alternative fragment length(s) may be 3,47,533 bps INFO @ Tue, 30 Jun 2020 02:41:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.20_model.r WARNING @ Tue, 30 Jun 2020 02:41:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:41:50: #2 You may need to consider one of the other alternative d(s): 3,47,533 WARNING @ Tue, 30 Jun 2020 02:41:50: #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 02:41:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:41:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:41:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.10_summits.bed INFO @ Tue, 30 Jun 2020 02:42:05: Done! pass1 - making usageList (261 chroms): 1 millis pass2 - checking and writing primary data (532 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:42:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:42:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:42:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:42:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669062/SRX4669062.20_summits.bed INFO @ Tue, 30 Jun 2020 02:42:29: Done! pass1 - making usageList (104 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 4 millis CompletedMACS2peakCalling