Job ID = 14170900 SRX = SRX8689059 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: 00:01:42 5347995 reads; of these: 5347995 (100.00%) were unpaired; of these: 170054 (3.18%) aligned 0 times 3709231 (69.36%) aligned exactly 1 time 1468710 (27.46%) aligned >1 times 96.82% overall alignment rate Time searching: 00:01:42 Overall time: 00:01:42 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] 417031 / 5177941 = 0.0805 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.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 @ Sat, 11 Dec 2021 09:01:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:01:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:01:30: 1000000 INFO @ Sat, 11 Dec 2021 09:01:37: 2000000 INFO @ Sat, 11 Dec 2021 09:01:44: 3000000 INFO @ Sat, 11 Dec 2021 09:01:51: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.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 @ Sat, 11 Dec 2021 09:01:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:01:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:01:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:01:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:01:56: #1 total tags in treatment: 4760910 INFO @ Sat, 11 Dec 2021 09:01:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:01:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:01:57: #1 tags after filtering in treatment: 4760907 INFO @ Sat, 11 Dec 2021 09:01:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:01:57: #1 finished! INFO @ Sat, 11 Dec 2021 09:01:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:01:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:01:57: #2 number of paired peaks: 362 WARNING @ Sat, 11 Dec 2021 09:01:57: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Sat, 11 Dec 2021 09:01:57: start model_add_line... INFO @ Sat, 11 Dec 2021 09:01:57: start X-correlation... INFO @ Sat, 11 Dec 2021 09:01:57: end of X-cor INFO @ Sat, 11 Dec 2021 09:01:57: #2 finished! INFO @ Sat, 11 Dec 2021 09:01:57: #2 predicted fragment length is 60 bps INFO @ Sat, 11 Dec 2021 09:01:57: #2 alternative fragment length(s) may be 60 bps INFO @ Sat, 11 Dec 2021 09:01:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.05_model.r WARNING @ Sat, 11 Dec 2021 09:01:57: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:01:57: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sat, 11 Dec 2021 09:01:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:01:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:01:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:02:01: 1000000 INFO @ Sat, 11 Dec 2021 09:02:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:02:08: 2000000 INFO @ Sat, 11 Dec 2021 09:02:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:02:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:02:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.05_summits.bed INFO @ Sat, 11 Dec 2021 09:02:13: Done! pass1 - making usageList (370 chroms): 1 millis pass2 - checking and writing primary data (839 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:02:15: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:02:23: 4000000 INFO @ Sat, 11 Dec 2021 09:02:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.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 @ Sat, 11 Dec 2021 09:02:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:02:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:02:29: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:02:29: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:02:29: #1 total tags in treatment: 4760910 INFO @ Sat, 11 Dec 2021 09:02:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:02:29: #1 tags after filtering in treatment: 4760907 INFO @ Sat, 11 Dec 2021 09:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:02:29: #1 finished! INFO @ Sat, 11 Dec 2021 09:02:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:02:30: #2 number of paired peaks: 362 WARNING @ Sat, 11 Dec 2021 09:02:30: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Sat, 11 Dec 2021 09:02:30: start model_add_line... INFO @ Sat, 11 Dec 2021 09:02:30: start X-correlation... INFO @ Sat, 11 Dec 2021 09:02:30: end of X-cor INFO @ Sat, 11 Dec 2021 09:02:30: #2 finished! INFO @ Sat, 11 Dec 2021 09:02:30: #2 predicted fragment length is 60 bps INFO @ Sat, 11 Dec 2021 09:02:30: #2 alternative fragment length(s) may be 60 bps INFO @ Sat, 11 Dec 2021 09:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.10_model.r WARNING @ Sat, 11 Dec 2021 09:02:30: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:02:30: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sat, 11 Dec 2021 09:02:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:02:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:02:30: 1000000 INFO @ Sat, 11 Dec 2021 09:02:37: 2000000 INFO @ Sat, 11 Dec 2021 09:02:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:02:43: 3000000 INFO @ Sat, 11 Dec 2021 09:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:02:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.10_summits.bed INFO @ Sat, 11 Dec 2021 09:02:45: Done! pass1 - making usageList (171 chroms): 2 millis pass2 - checking and writing primary data (347 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:02:50: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:02:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:02:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:02:56: #1 total tags in treatment: 4760910 INFO @ Sat, 11 Dec 2021 09:02:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:02:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:02:56: #1 tags after filtering in treatment: 4760907 INFO @ Sat, 11 Dec 2021 09:02:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:02:56: #1 finished! INFO @ Sat, 11 Dec 2021 09:02:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:02:57: #2 number of paired peaks: 362 WARNING @ Sat, 11 Dec 2021 09:02:57: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Sat, 11 Dec 2021 09:02:57: start model_add_line... INFO @ Sat, 11 Dec 2021 09:02:57: start X-correlation... INFO @ Sat, 11 Dec 2021 09:02:57: end of X-cor INFO @ Sat, 11 Dec 2021 09:02:57: #2 finished! INFO @ Sat, 11 Dec 2021 09:02:57: #2 predicted fragment length is 60 bps INFO @ Sat, 11 Dec 2021 09:02:57: #2 alternative fragment length(s) may be 60 bps INFO @ Sat, 11 Dec 2021 09:02:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.20_model.r WARNING @ Sat, 11 Dec 2021 09:02:57: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:02:57: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sat, 11 Dec 2021 09:02:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:02:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:02:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:03:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689059/SRX8689059.20_summits.bed INFO @ Sat, 11 Dec 2021 09:03:12: Done! pass1 - making usageList (101 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 7 millis CompletedMACS2peakCalling