Job ID = 14170893 SRX = SRX8689052 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: 00:01:23 6005350 reads; of these: 6005350 (100.00%) were unpaired; of these: 1145824 (19.08%) aligned 0 times 4024171 (67.01%) aligned exactly 1 time 835355 (13.91%) aligned >1 times 80.92% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 249410 / 4859526 = 0.0513 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 09:00:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.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 09:00:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:00:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:00:07: 1000000 INFO @ Sat, 11 Dec 2021 09:00:12: 2000000 INFO @ Sat, 11 Dec 2021 09:00:17: 3000000 INFO @ Sat, 11 Dec 2021 09:00:23: 4000000 INFO @ Sat, 11 Dec 2021 09:00:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:00:26: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:00:26: #1 total tags in treatment: 4610116 INFO @ Sat, 11 Dec 2021 09:00:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:00:26: #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 09:00:27: #1 tags after filtering in treatment: 4610061 INFO @ Sat, 11 Dec 2021 09:00:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:00:27: #1 finished! INFO @ Sat, 11 Dec 2021 09:00:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:00:27: #2 number of paired peaks: 126 WARNING @ Sat, 11 Dec 2021 09:00:27: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 11 Dec 2021 09:00:27: start model_add_line... INFO @ Sat, 11 Dec 2021 09:00:27: start X-correlation... INFO @ Sat, 11 Dec 2021 09:00:27: end of X-cor INFO @ Sat, 11 Dec 2021 09:00:27: #2 finished! INFO @ Sat, 11 Dec 2021 09:00:27: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Dec 2021 09:00:27: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 11 Dec 2021 09:00:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.05_model.r WARNING @ Sat, 11 Dec 2021 09:00:27: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:00:27: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 11 Dec 2021 09:00:27: #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 09:00:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:00:27: #3 Pre-compute pvalue-qvalue table... 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 09:00:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.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 09:00:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:00:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:00:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:00:38: 1000000 INFO @ Sat, 11 Dec 2021 09:00:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:00:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:00:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.05_summits.bed INFO @ Sat, 11 Dec 2021 09:00:42: Done! pass1 - making usageList (101 chroms): 0 millis pass2 - checking and writing primary data (238 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:00:44: 2000000 INFO @ Sat, 11 Dec 2021 09:00:50: 3000000 INFO @ Sat, 11 Dec 2021 09:00:57: 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 09:01:01: #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: 4610116 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: 4610061 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: 126 WARNING @ Sat, 11 Dec 2021 09:01:01: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 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 54 bps INFO @ Sat, 11 Dec 2021 09:01:01: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 11 Dec 2021 09:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.10_model.r WARNING @ Sat, 11 Dec 2021 09:01:01: #2 Since the d (54) 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): 54 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 09:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.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 09:01:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:01:03: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:01:09: 1000000 INFO @ Sat, 11 Dec 2021 09:01:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:01:16: 2000000 INFO @ Sat, 11 Dec 2021 09:01:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:01:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:01:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.10_summits.bed INFO @ Sat, 11 Dec 2021 09:01:16: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:01:22: 3000000 INFO @ Sat, 11 Dec 2021 09:01:29: 4000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:01:33: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:01:33: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:01:33: #1 total tags in treatment: 4610116 INFO @ Sat, 11 Dec 2021 09:01:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:01:33: #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 09:01:33: #1 tags after filtering in treatment: 4610061 INFO @ Sat, 11 Dec 2021 09:01:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:01:33: #1 finished! INFO @ Sat, 11 Dec 2021 09:01:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:01:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:01:34: #2 number of paired peaks: 126 WARNING @ Sat, 11 Dec 2021 09:01:34: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 11 Dec 2021 09:01:34: start model_add_line... INFO @ Sat, 11 Dec 2021 09:01:34: start X-correlation... INFO @ Sat, 11 Dec 2021 09:01:34: end of X-cor INFO @ Sat, 11 Dec 2021 09:01:34: #2 finished! INFO @ Sat, 11 Dec 2021 09:01:34: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Dec 2021 09:01:34: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 11 Dec 2021 09:01:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.20_model.r WARNING @ Sat, 11 Dec 2021 09:01:34: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:01:34: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 11 Dec 2021 09:01:34: #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 09:01:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:01:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:01:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:01:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:01:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:01:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689052/SRX8689052.20_summits.bed INFO @ Sat, 11 Dec 2021 09:01:49: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (79 records, 4 fields): 3 millis CompletedMACS2peakCalling