Job ID = 14167823 SRX = SRX8688911 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: 00:02:41 7173470 reads; of these: 7173470 (100.00%) were unpaired; of these: 590044 (8.23%) aligned 0 times 4521326 (63.03%) aligned exactly 1 time 2062100 (28.75%) aligned >1 times 91.77% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 612701 / 6583426 = 0.0931 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 @ Fri, 10 Dec 2021 13:36:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.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 @ Fri, 10 Dec 2021 13:36:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:36:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:36:49: 1000000 INFO @ Fri, 10 Dec 2021 13:36:57: 2000000 INFO @ Fri, 10 Dec 2021 13:37:04: 3000000 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 @ Fri, 10 Dec 2021 13:37:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.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 @ Fri, 10 Dec 2021 13:37:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:37:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:37:13: 4000000 INFO @ Fri, 10 Dec 2021 13:37:20: 1000000 INFO @ Fri, 10 Dec 2021 13:37:22: 5000000 INFO @ Fri, 10 Dec 2021 13:37:29: 2000000 INFO @ Fri, 10 Dec 2021 13:37:31: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:37:31: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:37:31: #1 total tags in treatment: 5970725 INFO @ Fri, 10 Dec 2021 13:37:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:37:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:37:32: #1 tags after filtering in treatment: 5970723 INFO @ Fri, 10 Dec 2021 13:37:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:37:32: #1 finished! INFO @ Fri, 10 Dec 2021 13:37:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:37:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:37:33: #2 number of paired peaks: 418 WARNING @ Fri, 10 Dec 2021 13:37:33: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Fri, 10 Dec 2021 13:37:33: start model_add_line... INFO @ Fri, 10 Dec 2021 13:37:33: start X-correlation... INFO @ Fri, 10 Dec 2021 13:37:33: end of X-cor INFO @ Fri, 10 Dec 2021 13:37:33: #2 finished! INFO @ Fri, 10 Dec 2021 13:37:33: #2 predicted fragment length is 55 bps INFO @ Fri, 10 Dec 2021 13:37:33: #2 alternative fragment length(s) may be 55 bps INFO @ Fri, 10 Dec 2021 13:37:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.05_model.r WARNING @ Fri, 10 Dec 2021 13:37:33: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:37:33: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Fri, 10 Dec 2021 13:37:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:37:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:37:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:37:38: 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 @ Fri, 10 Dec 2021 13:37:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.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 @ Fri, 10 Dec 2021 13:37:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:37:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:37:46: 4000000 INFO @ Fri, 10 Dec 2021 13:37:50: 1000000 INFO @ Fri, 10 Dec 2021 13:37:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:37:55: 5000000 INFO @ Fri, 10 Dec 2021 13:37:59: 2000000 INFO @ Fri, 10 Dec 2021 13:38:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:38:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:38:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.05_summits.bed INFO @ Fri, 10 Dec 2021 13:38:00: Done! pass1 - making usageList (491 chroms): 2 millis pass2 - checking and writing primary data (1272 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:38:03: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:38:03: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:38:03: #1 total tags in treatment: 5970725 INFO @ Fri, 10 Dec 2021 13:38:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:38:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:38:04: #1 tags after filtering in treatment: 5970723 INFO @ Fri, 10 Dec 2021 13:38:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:38:04: #1 finished! INFO @ Fri, 10 Dec 2021 13:38:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:38:04: #2 number of paired peaks: 418 WARNING @ Fri, 10 Dec 2021 13:38:04: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Fri, 10 Dec 2021 13:38:04: start model_add_line... INFO @ Fri, 10 Dec 2021 13:38:04: start X-correlation... INFO @ Fri, 10 Dec 2021 13:38:04: end of X-cor INFO @ Fri, 10 Dec 2021 13:38:04: #2 finished! INFO @ Fri, 10 Dec 2021 13:38:04: #2 predicted fragment length is 55 bps INFO @ Fri, 10 Dec 2021 13:38:04: #2 alternative fragment length(s) may be 55 bps INFO @ Fri, 10 Dec 2021 13:38:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.10_model.r WARNING @ Fri, 10 Dec 2021 13:38:04: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:38:04: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Fri, 10 Dec 2021 13:38:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:38:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:38:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:38:09: 3000000 INFO @ Fri, 10 Dec 2021 13:38:18: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:38:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:38:27: 5000000 INFO @ Fri, 10 Dec 2021 13:38:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:38:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:38:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.10_summits.bed INFO @ Fri, 10 Dec 2021 13:38:31: Done! pass1 - making usageList (232 chroms): 2 millis pass2 - checking and writing primary data (487 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:38:37: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 13:38:37: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 13:38:37: #1 total tags in treatment: 5970725 INFO @ Fri, 10 Dec 2021 13:38:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:38:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:38:37: #1 tags after filtering in treatment: 5970723 INFO @ Fri, 10 Dec 2021 13:38:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:38:37: #1 finished! INFO @ Fri, 10 Dec 2021 13:38:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:38:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:38:38: #2 number of paired peaks: 418 WARNING @ Fri, 10 Dec 2021 13:38:38: Fewer paired peaks (418) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 418 pairs to build model! INFO @ Fri, 10 Dec 2021 13:38:38: start model_add_line... INFO @ Fri, 10 Dec 2021 13:38:38: start X-correlation... INFO @ Fri, 10 Dec 2021 13:38:38: end of X-cor INFO @ Fri, 10 Dec 2021 13:38:38: #2 finished! INFO @ Fri, 10 Dec 2021 13:38:38: #2 predicted fragment length is 55 bps INFO @ Fri, 10 Dec 2021 13:38:38: #2 alternative fragment length(s) may be 55 bps INFO @ Fri, 10 Dec 2021 13:38:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.20_model.r WARNING @ Fri, 10 Dec 2021 13:38:38: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:38:38: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Fri, 10 Dec 2021 13:38:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:38:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:38:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:38:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:39:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:39:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:39:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688911/SRX8688911.20_summits.bed INFO @ Fri, 10 Dec 2021 13:39:05: Done! pass1 - making usageList (108 chroms): 2 millis pass2 - checking and writing primary data (216 records, 4 fields): 10 millis CompletedMACS2peakCalling