Job ID = 6627538 SRX = SRX8521371 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: 00:05:04 36937163 reads; of these: 36937163 (100.00%) were unpaired; of these: 31992238 (86.61%) aligned 0 times 3668888 (9.93%) aligned exactly 1 time 1276037 (3.45%) aligned >1 times 13.39% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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_rmdupse_core] 674669 / 4944925 = 0.1364 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, 14 Jul 2020 12:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.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, 14 Jul 2020 12:01:41: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:01:41: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:01:48: 1000000 INFO @ Tue, 14 Jul 2020 12:01:54: 2000000 INFO @ Tue, 14 Jul 2020 12:02:01: 3000000 INFO @ Tue, 14 Jul 2020 12:02:08: 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, 14 Jul 2020 12:02:09: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:02:09: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:02:09: #1 total tags in treatment: 4270256 INFO @ Tue, 14 Jul 2020 12:02:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:02:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:02:10: #1 tags after filtering in treatment: 4270034 INFO @ Tue, 14 Jul 2020 12:02:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:02:10: #1 finished! INFO @ Tue, 14 Jul 2020 12:02:10: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:02:10: #2 number of paired peaks: 758 WARNING @ Tue, 14 Jul 2020 12:02:10: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Tue, 14 Jul 2020 12:02:10: start model_add_line... INFO @ Tue, 14 Jul 2020 12:02:10: start X-correlation... INFO @ Tue, 14 Jul 2020 12:02:10: end of X-cor INFO @ Tue, 14 Jul 2020 12:02:10: #2 finished! INFO @ Tue, 14 Jul 2020 12:02:10: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 12:02:10: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 12:02:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.05_model.r WARNING @ Tue, 14 Jul 2020 12:02:10: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:02:10: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 12:02:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:02:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:02:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:02:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.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, 14 Jul 2020 12:02:11: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:02:11: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:02:16: 1000000 INFO @ Tue, 14 Jul 2020 12:02:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:02:21: 2000000 INFO @ Tue, 14 Jul 2020 12:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.05_summits.bed INFO @ Tue, 14 Jul 2020 12:02:24: Done! pass1 - making usageList (236 chroms): 1 millis pass2 - checking and writing primary data (1036 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:02:27: 3000000 INFO @ Tue, 14 Jul 2020 12:02:32: 4000000 INFO @ Tue, 14 Jul 2020 12:02:34: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:02:34: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:02:34: #1 total tags in treatment: 4270256 INFO @ Tue, 14 Jul 2020 12:02:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:02:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:02:34: #1 tags after filtering in treatment: 4270034 INFO @ Tue, 14 Jul 2020 12:02:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:02:34: #1 finished! INFO @ Tue, 14 Jul 2020 12:02:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:02:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:02:34: #2 number of paired peaks: 758 WARNING @ Tue, 14 Jul 2020 12:02:34: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Tue, 14 Jul 2020 12:02:34: start model_add_line... INFO @ Tue, 14 Jul 2020 12:02:35: start X-correlation... INFO @ Tue, 14 Jul 2020 12:02:35: end of X-cor INFO @ Tue, 14 Jul 2020 12:02:35: #2 finished! INFO @ Tue, 14 Jul 2020 12:02:35: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 12:02:35: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 12:02:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.10_model.r WARNING @ Tue, 14 Jul 2020 12:02:35: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:02:35: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 12:02:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:02:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:02:35: #3 Pre-compute pvalue-qvalue table... 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, 14 Jul 2020 12:02:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.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, 14 Jul 2020 12:02:41: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:02:41: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:02:44: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:02:48: 1000000 INFO @ Tue, 14 Jul 2020 12:02:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:02:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:02:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.10_summits.bed INFO @ Tue, 14 Jul 2020 12:02:48: Done! pass1 - making usageList (135 chroms): 1 millis pass2 - checking and writing primary data (410 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:02:54: 2000000 INFO @ Tue, 14 Jul 2020 12:03:01: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:03:10: 4000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:03:12: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:03:12: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:03:12: #1 total tags in treatment: 4270256 INFO @ Tue, 14 Jul 2020 12:03:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:03:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:03:13: #1 tags after filtering in treatment: 4270034 INFO @ Tue, 14 Jul 2020 12:03:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:03:13: #1 finished! INFO @ Tue, 14 Jul 2020 12:03:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:03:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:03:13: #2 number of paired peaks: 758 WARNING @ Tue, 14 Jul 2020 12:03:13: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Tue, 14 Jul 2020 12:03:13: start model_add_line... INFO @ Tue, 14 Jul 2020 12:03:13: start X-correlation... INFO @ Tue, 14 Jul 2020 12:03:13: end of X-cor INFO @ Tue, 14 Jul 2020 12:03:13: #2 finished! INFO @ Tue, 14 Jul 2020 12:03:13: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 12:03:13: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 12:03:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.20_model.r WARNING @ Tue, 14 Jul 2020 12:03:13: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:03:13: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 12:03:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:03:13: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:03:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:03:23: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:03:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:03:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:03:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521371/SRX8521371.20_summits.bed INFO @ Tue, 14 Jul 2020 12:03:28: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (138 records, 4 fields): 3 millis CompletedMACS2peakCalling