Job ID = 6627546 SRX = SRX8521358 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: 00:10:49 61764724 reads; of these: 61764724 (100.00%) were unpaired; of these: 54957289 (88.98%) aligned 0 times 4965234 (8.04%) aligned exactly 1 time 1842201 (2.98%) aligned >1 times 11.02% overall alignment rate Time searching: 00:10:49 Overall time: 00:10:49 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] 1213678 / 6807435 = 0.1783 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 12:10:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.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 12:10:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:10:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:10:32: 1000000 INFO @ Tue, 14 Jul 2020 12:10:38: 2000000 INFO @ Tue, 14 Jul 2020 12:10:44: 3000000 INFO @ Tue, 14 Jul 2020 12:10:50: 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 12:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.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 12:10:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:10:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:10:56: 5000000 INFO @ Tue, 14 Jul 2020 12:11:00: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 12:11:00: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 12:11:00: #1 total tags in treatment: 5593757 INFO @ Tue, 14 Jul 2020 12:11:00: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:11:00: #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 12:11:00: #1 tags after filtering in treatment: 5593551 INFO @ Tue, 14 Jul 2020 12:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:11:00: #1 finished! INFO @ Tue, 14 Jul 2020 12:11:00: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:11:01: #2 number of paired peaks: 829 WARNING @ Tue, 14 Jul 2020 12:11:01: Fewer paired peaks (829) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 829 pairs to build model! INFO @ Tue, 14 Jul 2020 12:11:01: start model_add_line... INFO @ Tue, 14 Jul 2020 12:11:01: start X-correlation... INFO @ Tue, 14 Jul 2020 12:11:01: end of X-cor INFO @ Tue, 14 Jul 2020 12:11:01: #2 finished! INFO @ Tue, 14 Jul 2020 12:11:01: #2 predicted fragment length is 74 bps INFO @ Tue, 14 Jul 2020 12:11:01: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 14 Jul 2020 12:11:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.05_model.r WARNING @ Tue, 14 Jul 2020 12:11:01: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:11:01: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 14 Jul 2020 12:11:01: #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 12:11:01: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:11:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:11:06: 1000000 INFO @ Tue, 14 Jul 2020 12:11:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:11:16: 2000000 INFO @ Tue, 14 Jul 2020 12:11:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:11:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:11:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.05_summits.bed INFO @ Tue, 14 Jul 2020 12:11:21: Done! pass1 - making usageList (225 chroms): 1 millis pass2 - checking and writing primary data (1732 records, 4 fields): 9 millis CompletedMACS2peakCalling 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 12:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.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 12:11:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:11:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:11:26: 3000000 INFO @ Tue, 14 Jul 2020 12:11:32: 1000000 INFO @ Tue, 14 Jul 2020 12:11:35: 4000000 INFO @ Tue, 14 Jul 2020 12:11:39: 2000000 INFO @ Tue, 14 Jul 2020 12:11:45: 5000000 INFO @ Tue, 14 Jul 2020 12:11:45: 3000000 INFO @ Tue, 14 Jul 2020 12:11:50: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 12:11:50: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 12:11:50: #1 total tags in treatment: 5593757 INFO @ Tue, 14 Jul 2020 12:11:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:11:50: #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 12:11:51: #1 tags after filtering in treatment: 5593551 INFO @ Tue, 14 Jul 2020 12:11:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:11:51: #1 finished! INFO @ Tue, 14 Jul 2020 12:11:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:11:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:11:51: #2 number of paired peaks: 829 WARNING @ Tue, 14 Jul 2020 12:11:51: Fewer paired peaks (829) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 829 pairs to build model! INFO @ Tue, 14 Jul 2020 12:11:51: start model_add_line... INFO @ Tue, 14 Jul 2020 12:11:51: start X-correlation... INFO @ Tue, 14 Jul 2020 12:11:51: 4000000 INFO @ Tue, 14 Jul 2020 12:11:51: end of X-cor INFO @ Tue, 14 Jul 2020 12:11:51: #2 finished! INFO @ Tue, 14 Jul 2020 12:11:51: #2 predicted fragment length is 74 bps INFO @ Tue, 14 Jul 2020 12:11:51: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 14 Jul 2020 12:11:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.10_model.r WARNING @ Tue, 14 Jul 2020 12:11:51: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:11:51: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 14 Jul 2020 12:11:51: #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 12:11:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:11:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:11:58: 5000000 INFO @ Tue, 14 Jul 2020 12:12:02: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 12:12:02: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 12:12:02: #1 total tags in treatment: 5593757 INFO @ Tue, 14 Jul 2020 12:12:02: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:12:02: #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 12:12:02: #1 tags after filtering in treatment: 5593551 INFO @ Tue, 14 Jul 2020 12:12:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:12:02: #1 finished! INFO @ Tue, 14 Jul 2020 12:12:02: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:12:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:12:03: #2 number of paired peaks: 829 WARNING @ Tue, 14 Jul 2020 12:12:03: Fewer paired peaks (829) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 829 pairs to build model! INFO @ Tue, 14 Jul 2020 12:12:03: start model_add_line... INFO @ Tue, 14 Jul 2020 12:12:03: start X-correlation... INFO @ Tue, 14 Jul 2020 12:12:03: end of X-cor INFO @ Tue, 14 Jul 2020 12:12:03: #2 finished! INFO @ Tue, 14 Jul 2020 12:12:03: #2 predicted fragment length is 74 bps INFO @ Tue, 14 Jul 2020 12:12:03: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 14 Jul 2020 12:12:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.20_model.r WARNING @ Tue, 14 Jul 2020 12:12:03: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:12:03: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 14 Jul 2020 12:12:03: #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 12:12:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:12:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:12:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:12:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.10_summits.bed INFO @ Tue, 14 Jul 2020 12:12:14: Done! pass1 - making usageList (154 chroms): 1 millis pass2 - checking and writing primary data (616 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:12:17: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:12:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:12:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:12:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521358/SRX8521358.20_summits.bed INFO @ Tue, 14 Jul 2020 12:12:24: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (233 records, 4 fields): 5 millis CompletedMACS2peakCalling