Job ID = 14170890 SRX = SRX8689053 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: 00:01:30 6470184 reads; of these: 6470184 (100.00%) were unpaired; of these: 501791 (7.76%) aligned 0 times 5201283 (80.39%) aligned exactly 1 time 767110 (11.86%) aligned >1 times 92.24% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 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] 290701 / 5968393 = 0.0487 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 08:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.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 08:59:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:59:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:59:59: 1000000 INFO @ Sat, 11 Dec 2021 09:00:06: 2000000 INFO @ Sat, 11 Dec 2021 09:00:13: 3000000 INFO @ Sat, 11 Dec 2021 09:00:20: 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 09:00:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.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 09:00:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:00:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:00:28: 5000000 INFO @ Sat, 11 Dec 2021 09:00:30: 1000000 INFO @ Sat, 11 Dec 2021 09:00:33: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:00:33: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:00:33: #1 total tags in treatment: 5677692 INFO @ Sat, 11 Dec 2021 09:00:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:00:33: #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 09:00:33: #1 tags after filtering in treatment: 5677438 INFO @ Sat, 11 Dec 2021 09:00:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:00:33: #1 finished! INFO @ Sat, 11 Dec 2021 09:00:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:00:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:00:33: #2 number of paired peaks: 105 WARNING @ Sat, 11 Dec 2021 09:00:33: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 11 Dec 2021 09:00:33: start model_add_line... INFO @ Sat, 11 Dec 2021 09:00:33: start X-correlation... INFO @ Sat, 11 Dec 2021 09:00:33: end of X-cor INFO @ Sat, 11 Dec 2021 09:00:33: #2 finished! INFO @ Sat, 11 Dec 2021 09:00:33: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:00:33: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Dec 2021 09:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.05_model.r WARNING @ Sat, 11 Dec 2021 09:00:33: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:00:33: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Dec 2021 09:00:33: #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 09:00:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:00:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:00:36: 2000000 INFO @ Sat, 11 Dec 2021 09:00:43: 3000000 INFO @ Sat, 11 Dec 2021 09:00:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:00:49: 4000000 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 09:00:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:00:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:00:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.05_summits.bed INFO @ Sat, 11 Dec 2021 09:00:52: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (223 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:00:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.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 09:00:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:00:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:00:56: 5000000 INFO @ Sat, 11 Dec 2021 09:00:59: 1000000 INFO @ Sat, 11 Dec 2021 09:01:01: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:01:01: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:01:01: #1 total tags in treatment: 5677692 INFO @ Sat, 11 Dec 2021 09:01:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:01:01: #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 09:01:01: #1 tags after filtering in treatment: 5677438 INFO @ Sat, 11 Dec 2021 09:01:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:01:01: #1 finished! INFO @ Sat, 11 Dec 2021 09:01:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:01:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:01:01: #2 number of paired peaks: 105 WARNING @ Sat, 11 Dec 2021 09:01:01: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 11 Dec 2021 09:01:01: start model_add_line... INFO @ Sat, 11 Dec 2021 09:01:01: start X-correlation... INFO @ Sat, 11 Dec 2021 09:01:01: end of X-cor INFO @ Sat, 11 Dec 2021 09:01:01: #2 finished! INFO @ Sat, 11 Dec 2021 09:01:01: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:01:01: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Dec 2021 09:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.10_model.r WARNING @ Sat, 11 Dec 2021 09:01:01: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:01:01: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Dec 2021 09:01:01: #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 09:01:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:01:05: 2000000 INFO @ Sat, 11 Dec 2021 09:01:11: 3000000 INFO @ Sat, 11 Dec 2021 09:01:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:01:17: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:01:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:01:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:01:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.10_summits.bed INFO @ Sat, 11 Dec 2021 09:01:20: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:01:23: 5000000 INFO @ Sat, 11 Dec 2021 09:01:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:01:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:01:27: #1 total tags in treatment: 5677692 INFO @ Sat, 11 Dec 2021 09:01:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:01:27: #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 09:01:28: #1 tags after filtering in treatment: 5677438 INFO @ Sat, 11 Dec 2021 09:01:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:01:28: #1 finished! INFO @ Sat, 11 Dec 2021 09:01:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:01:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:01:28: #2 number of paired peaks: 105 WARNING @ Sat, 11 Dec 2021 09:01:28: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 11 Dec 2021 09:01:28: start model_add_line... INFO @ Sat, 11 Dec 2021 09:01:28: start X-correlation... INFO @ Sat, 11 Dec 2021 09:01:28: end of X-cor INFO @ Sat, 11 Dec 2021 09:01:28: #2 finished! INFO @ Sat, 11 Dec 2021 09:01:28: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:01:28: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Dec 2021 09:01:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.20_model.r WARNING @ Sat, 11 Dec 2021 09:01:28: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:01:28: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Dec 2021 09:01:28: #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 09:01:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:01:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:01:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:01:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:01:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:01:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689053/SRX8689053.20_summits.bed INFO @ Sat, 11 Dec 2021 09:01:46: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (69 records, 4 fields): 2 millis CompletedMACS2peakCalling