Job ID = 6627536 SRX = SRX8521368 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: 00:06:13 48386089 reads; of these: 48386089 (100.00%) were unpaired; of these: 41888279 (86.57%) aligned 0 times 4775577 (9.87%) aligned exactly 1 time 1722233 (3.56%) aligned >1 times 13.43% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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] 994824 / 6497810 = 0.1531 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 12:02:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.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 12:02:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:02:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:02:38: 1000000 INFO @ Tue, 14 Jul 2020 12:02:43: 2000000 INFO @ Tue, 14 Jul 2020 12:02:49: 3000000 INFO @ Tue, 14 Jul 2020 12:02:54: 4000000 INFO @ Tue, 14 Jul 2020 12:03:00: 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, 14 Jul 2020 12:03:03: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:03:03: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:03:03: #1 total tags in treatment: 5502986 INFO @ Tue, 14 Jul 2020 12:03:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:03:03: #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 12:03:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.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 12:03:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:03:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:03:03: #1 tags after filtering in treatment: 5502789 INFO @ Tue, 14 Jul 2020 12:03:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:03:03: #1 finished! INFO @ Tue, 14 Jul 2020 12:03:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:03:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:03:03: #2 number of paired peaks: 653 WARNING @ Tue, 14 Jul 2020 12:03:03: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Tue, 14 Jul 2020 12:03:03: start model_add_line... INFO @ Tue, 14 Jul 2020 12:03:03: start X-correlation... INFO @ Tue, 14 Jul 2020 12:03:03: end of X-cor INFO @ Tue, 14 Jul 2020 12:03:03: #2 finished! INFO @ Tue, 14 Jul 2020 12:03:03: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:03:03: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:03:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.05_model.r WARNING @ Tue, 14 Jul 2020 12:03:03: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:03:03: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:03:03: #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 12:03:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:03:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:03:09: 1000000 INFO @ Tue, 14 Jul 2020 12:03:15: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:03:15: 2000000 INFO @ Tue, 14 Jul 2020 12:03:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:03:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:03:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.05_summits.bed INFO @ Tue, 14 Jul 2020 12:03:21: Done! pass1 - making usageList (234 chroms): 1 millis pass2 - checking and writing primary data (1028 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:03:21: 3000000 INFO @ Tue, 14 Jul 2020 12:03:27: 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, 14 Jul 2020 12:03:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.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 12:03:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:03:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:03:33: 5000000 INFO @ Tue, 14 Jul 2020 12:03:36: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:03:36: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:03:36: #1 total tags in treatment: 5502986 INFO @ Tue, 14 Jul 2020 12:03:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:03:36: #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 12:03:36: #1 tags after filtering in treatment: 5502789 INFO @ Tue, 14 Jul 2020 12:03:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:03:36: #1 finished! INFO @ Tue, 14 Jul 2020 12:03:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:03:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:03:37: #2 number of paired peaks: 653 WARNING @ Tue, 14 Jul 2020 12:03:37: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Tue, 14 Jul 2020 12:03:37: start model_add_line... INFO @ Tue, 14 Jul 2020 12:03:37: start X-correlation... INFO @ Tue, 14 Jul 2020 12:03:37: end of X-cor INFO @ Tue, 14 Jul 2020 12:03:37: #2 finished! INFO @ Tue, 14 Jul 2020 12:03:37: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:03:37: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.10_model.r WARNING @ Tue, 14 Jul 2020 12:03:37: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:03:37: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:03:37: #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 12:03:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:03:38: 1000000 INFO @ Tue, 14 Jul 2020 12:03:44: 2000000 INFO @ Tue, 14 Jul 2020 12:03:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:03:50: 3000000 INFO @ Tue, 14 Jul 2020 12:03:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:03:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:03:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.10_summits.bed INFO @ Tue, 14 Jul 2020 12:03:55: Done! pass1 - making usageList (142 chroms): 1 millis pass2 - checking and writing primary data (424 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:03:55: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:04:01: 5000000 INFO @ Tue, 14 Jul 2020 12:04:04: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:04:04: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:04:04: #1 total tags in treatment: 5502986 INFO @ Tue, 14 Jul 2020 12:04:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:04:04: #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 12:04:04: #1 tags after filtering in treatment: 5502789 INFO @ Tue, 14 Jul 2020 12:04:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:04:04: #1 finished! INFO @ Tue, 14 Jul 2020 12:04:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:04:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:04:04: #2 number of paired peaks: 653 WARNING @ Tue, 14 Jul 2020 12:04:04: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Tue, 14 Jul 2020 12:04:04: start model_add_line... INFO @ Tue, 14 Jul 2020 12:04:04: start X-correlation... INFO @ Tue, 14 Jul 2020 12:04:04: end of X-cor INFO @ Tue, 14 Jul 2020 12:04:04: #2 finished! INFO @ Tue, 14 Jul 2020 12:04:04: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:04:04: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:04:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.20_model.r WARNING @ Tue, 14 Jul 2020 12:04:04: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:04:04: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:04:04: #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 12:04:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:04:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:04:16: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:04:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:04:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:04:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521368/SRX8521368.20_summits.bed INFO @ Tue, 14 Jul 2020 12:04:22: Done! pass1 - making usageList (84 chroms): 1 millis pass2 - checking and writing primary data (158 records, 4 fields): 3 millis CompletedMACS2peakCalling