Job ID = 6627451 SRX = SRX8521311 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: 00:09:52 56961720 reads; of these: 56961720 (100.00%) were unpaired; of these: 45485782 (79.85%) aligned 0 times 7830589 (13.75%) aligned exactly 1 time 3645349 (6.40%) aligned >1 times 20.15% overall alignment rate Time searching: 00:09:52 Overall time: 00:09:52 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] 2593991 / 11475938 = 0.2260 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 11:47:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.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 11:47:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:47:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:47:31: 1000000 INFO @ Tue, 14 Jul 2020 11:47:37: 2000000 INFO @ Tue, 14 Jul 2020 11:47:43: 3000000 INFO @ Tue, 14 Jul 2020 11:47:48: 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 11:47:54: 5000000 INFO @ Tue, 14 Jul 2020 11:47:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.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 11:47:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:47:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:48:00: 6000000 INFO @ Tue, 14 Jul 2020 11:48:03: 1000000 INFO @ Tue, 14 Jul 2020 11:48:06: 7000000 INFO @ Tue, 14 Jul 2020 11:48:11: 2000000 INFO @ Tue, 14 Jul 2020 11:48:12: 8000000 INFO @ Tue, 14 Jul 2020 11:48:17: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 11:48:17: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 11:48:17: #1 total tags in treatment: 8881947 INFO @ Tue, 14 Jul 2020 11:48:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:48:17: #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 11:48:18: 3000000 INFO @ Tue, 14 Jul 2020 11:48:18: #1 tags after filtering in treatment: 8881819 INFO @ Tue, 14 Jul 2020 11:48:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:48:18: #1 finished! INFO @ Tue, 14 Jul 2020 11:48:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:48:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:48:19: #2 number of paired peaks: 359 WARNING @ Tue, 14 Jul 2020 11:48:19: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 14 Jul 2020 11:48:19: start model_add_line... INFO @ Tue, 14 Jul 2020 11:48:19: start X-correlation... INFO @ Tue, 14 Jul 2020 11:48:19: end of X-cor INFO @ Tue, 14 Jul 2020 11:48:19: #2 finished! INFO @ Tue, 14 Jul 2020 11:48:19: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 11:48:19: #2 alternative fragment length(s) may be 4,11,57,71,521,526,571 bps INFO @ Tue, 14 Jul 2020 11:48:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.05_model.r WARNING @ Tue, 14 Jul 2020 11:48:19: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:48:19: #2 You may need to consider one of the other alternative d(s): 4,11,57,71,521,526,571 WARNING @ Tue, 14 Jul 2020 11:48:19: #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 11:48:19: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:48:19: #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 11:48:25: 4000000 INFO @ Tue, 14 Jul 2020 11:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.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 11:48:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:48:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:48:32: 5000000 INFO @ Tue, 14 Jul 2020 11:48:32: 1000000 INFO @ Tue, 14 Jul 2020 11:48:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:48:39: 2000000 INFO @ Tue, 14 Jul 2020 11:48:39: 6000000 INFO @ Tue, 14 Jul 2020 11:48:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:48:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:48:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.05_summits.bed INFO @ Tue, 14 Jul 2020 11:48:46: Done! INFO @ Tue, 14 Jul 2020 11:48:47: 3000000 pass1 - making usageList (306 chroms): 0 millis pass2 - checking and writing primary data (830 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:48:47: 7000000 INFO @ Tue, 14 Jul 2020 11:48:53: 4000000 INFO @ Tue, 14 Jul 2020 11:48:55: 8000000 INFO @ Tue, 14 Jul 2020 11:49:00: 5000000 INFO @ Tue, 14 Jul 2020 11:49:01: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 11:49:01: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 11:49:01: #1 total tags in treatment: 8881947 INFO @ Tue, 14 Jul 2020 11:49:01: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:49:01: #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 11:49:02: #1 tags after filtering in treatment: 8881819 INFO @ Tue, 14 Jul 2020 11:49:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:49:02: #1 finished! INFO @ Tue, 14 Jul 2020 11:49:02: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:49:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:49:02: #2 number of paired peaks: 359 WARNING @ Tue, 14 Jul 2020 11:49:02: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 14 Jul 2020 11:49:02: start model_add_line... INFO @ Tue, 14 Jul 2020 11:49:02: start X-correlation... INFO @ Tue, 14 Jul 2020 11:49:02: end of X-cor INFO @ Tue, 14 Jul 2020 11:49:02: #2 finished! INFO @ Tue, 14 Jul 2020 11:49:02: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 11:49:02: #2 alternative fragment length(s) may be 4,11,57,71,521,526,571 bps INFO @ Tue, 14 Jul 2020 11:49:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.10_model.r WARNING @ Tue, 14 Jul 2020 11:49:02: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:49:02: #2 You may need to consider one of the other alternative d(s): 4,11,57,71,521,526,571 WARNING @ Tue, 14 Jul 2020 11:49:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:49:02: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:49:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:49:07: 6000000 INFO @ Tue, 14 Jul 2020 11:49:14: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:49:21: 8000000 INFO @ Tue, 14 Jul 2020 11:49:23: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:49:27: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 11:49:27: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 11:49:27: #1 total tags in treatment: 8881947 INFO @ Tue, 14 Jul 2020 11:49:27: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:49:27: #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 11:49:27: #1 tags after filtering in treatment: 8881819 INFO @ Tue, 14 Jul 2020 11:49:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:49:27: #1 finished! INFO @ Tue, 14 Jul 2020 11:49:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:49:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:49:28: #2 number of paired peaks: 359 WARNING @ Tue, 14 Jul 2020 11:49:28: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 14 Jul 2020 11:49:28: start model_add_line... INFO @ Tue, 14 Jul 2020 11:49:28: start X-correlation... INFO @ Tue, 14 Jul 2020 11:49:28: end of X-cor INFO @ Tue, 14 Jul 2020 11:49:28: #2 finished! INFO @ Tue, 14 Jul 2020 11:49:28: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 11:49:28: #2 alternative fragment length(s) may be 4,11,57,71,521,526,571 bps INFO @ Tue, 14 Jul 2020 11:49:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.20_model.r WARNING @ Tue, 14 Jul 2020 11:49:28: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:49:28: #2 You may need to consider one of the other alternative d(s): 4,11,57,71,521,526,571 WARNING @ Tue, 14 Jul 2020 11:49:28: #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 11:49:28: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:49:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:49:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:49:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:49:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.10_summits.bed INFO @ Tue, 14 Jul 2020 11:49:33: Done! pass1 - making usageList (142 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:49:46: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521311/SRX8521311.20_summits.bed INFO @ Tue, 14 Jul 2020 11:49:55: Done! pass1 - making usageList (91 chroms): 0 millis pass2 - checking and writing primary data (167 records, 4 fields): 6 millis CompletedMACS2peakCalling