Job ID = 14168778 SRX = SRX8688972 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:59 6523145 reads; of these: 6523145 (100.00%) were unpaired; of these: 422605 (6.48%) aligned 0 times 3974815 (60.93%) aligned exactly 1 time 2125725 (32.59%) aligned >1 times 93.52% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 693138 / 6100540 = 0.1136 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 20:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.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 20:10:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:10:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:11:00: 1000000 INFO @ Fri, 10 Dec 2021 20:11:05: 2000000 INFO @ Fri, 10 Dec 2021 20:11:10: 3000000 INFO @ Fri, 10 Dec 2021 20:11:15: 4000000 INFO @ Fri, 10 Dec 2021 20:11:20: 5000000 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 20:11:22: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 20:11:22: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 20:11:22: #1 total tags in treatment: 5407402 INFO @ Fri, 10 Dec 2021 20:11:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:11:22: #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 20:11:23: #1 tags after filtering in treatment: 5407399 INFO @ Fri, 10 Dec 2021 20:11:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 20:11:23: #1 finished! INFO @ Fri, 10 Dec 2021 20:11:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:11:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:11:23: #2 number of paired peaks: 514 WARNING @ Fri, 10 Dec 2021 20:11:23: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Fri, 10 Dec 2021 20:11:23: start model_add_line... INFO @ Fri, 10 Dec 2021 20:11:23: start X-correlation... INFO @ Fri, 10 Dec 2021 20:11:23: end of X-cor INFO @ Fri, 10 Dec 2021 20:11:23: #2 finished! INFO @ Fri, 10 Dec 2021 20:11:23: #2 predicted fragment length is 61 bps INFO @ Fri, 10 Dec 2021 20:11:23: #2 alternative fragment length(s) may be 61 bps INFO @ Fri, 10 Dec 2021 20:11:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.05_model.r WARNING @ Fri, 10 Dec 2021 20:11:23: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:11:23: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Fri, 10 Dec 2021 20:11:23: #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 20:11:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:11:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:11:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.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 20:11:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:11:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:11:29: 1000000 INFO @ Fri, 10 Dec 2021 20:11:34: 2000000 INFO @ Fri, 10 Dec 2021 20:11:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:11:39: 3000000 INFO @ Fri, 10 Dec 2021 20:11:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:11:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:11:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.05_summits.bed INFO @ Fri, 10 Dec 2021 20:11:40: Done! pass1 - making usageList (587 chroms): 1 millis pass2 - checking and writing primary data (1453 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:11:44: 4000000 INFO @ Fri, 10 Dec 2021 20:11:49: 5000000 INFO @ Fri, 10 Dec 2021 20:11:51: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 20:11:51: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 20:11:51: #1 total tags in treatment: 5407402 INFO @ Fri, 10 Dec 2021 20:11:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:11:51: #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 20:11:52: #1 tags after filtering in treatment: 5407399 INFO @ Fri, 10 Dec 2021 20:11:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 20:11:52: #1 finished! INFO @ Fri, 10 Dec 2021 20:11:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:11:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:11:52: #2 number of paired peaks: 514 WARNING @ Fri, 10 Dec 2021 20:11:52: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Fri, 10 Dec 2021 20:11:52: start model_add_line... INFO @ Fri, 10 Dec 2021 20:11:52: start X-correlation... INFO @ Fri, 10 Dec 2021 20:11:52: end of X-cor INFO @ Fri, 10 Dec 2021 20:11:52: #2 finished! INFO @ Fri, 10 Dec 2021 20:11:52: #2 predicted fragment length is 61 bps INFO @ Fri, 10 Dec 2021 20:11:52: #2 alternative fragment length(s) may be 61 bps INFO @ Fri, 10 Dec 2021 20:11:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.10_model.r WARNING @ Fri, 10 Dec 2021 20:11:52: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:11:52: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Fri, 10 Dec 2021 20:11:52: #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 20:11:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:11:52: #3 Pre-compute pvalue-qvalue table... 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 20:11:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.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 20:11:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:11:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:11:59: 1000000 INFO @ Fri, 10 Dec 2021 20:12:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:12:04: 2000000 INFO @ Fri, 10 Dec 2021 20:12:09: 3000000 INFO @ Fri, 10 Dec 2021 20:12:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:12:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:12:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.10_summits.bed INFO @ Fri, 10 Dec 2021 20:12:09: Done! pass1 - making usageList (272 chroms): 1 millis pass2 - checking and writing primary data (525 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:12:14: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:12:19: 5000000 INFO @ Fri, 10 Dec 2021 20:12:22: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 20:12:22: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 20:12:22: #1 total tags in treatment: 5407402 INFO @ Fri, 10 Dec 2021 20:12:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:12:22: #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 20:12:22: #1 tags after filtering in treatment: 5407399 INFO @ Fri, 10 Dec 2021 20:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 20:12:22: #1 finished! INFO @ Fri, 10 Dec 2021 20:12:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:12:22: #2 number of paired peaks: 514 WARNING @ Fri, 10 Dec 2021 20:12:22: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Fri, 10 Dec 2021 20:12:22: start model_add_line... INFO @ Fri, 10 Dec 2021 20:12:22: start X-correlation... INFO @ Fri, 10 Dec 2021 20:12:22: end of X-cor INFO @ Fri, 10 Dec 2021 20:12:22: #2 finished! INFO @ Fri, 10 Dec 2021 20:12:22: #2 predicted fragment length is 61 bps INFO @ Fri, 10 Dec 2021 20:12:22: #2 alternative fragment length(s) may be 61 bps INFO @ Fri, 10 Dec 2021 20:12:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.20_model.r WARNING @ Fri, 10 Dec 2021 20:12:22: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:12:22: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Fri, 10 Dec 2021 20:12:22: #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 20:12:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:12:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:12:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:12:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:12:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:12:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688972/SRX8688972.20_summits.bed INFO @ Fri, 10 Dec 2021 20:12:39: Done! pass1 - making usageList (120 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 9 millis CompletedMACS2peakCalling