Job ID = 14170960 SRX = SRX8689092 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: 00:01:53 6135217 reads; of these: 6135217 (100.00%) were unpaired; of these: 210509 (3.43%) aligned 0 times 3972367 (64.75%) aligned exactly 1 time 1952341 (31.82%) aligned >1 times 96.57% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 448245 / 5924708 = 0.0757 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 09:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.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 09:08:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:08:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:08:52: 1000000 INFO @ Sat, 11 Dec 2021 09:08:58: 2000000 INFO @ Sat, 11 Dec 2021 09:09:04: 3000000 INFO @ Sat, 11 Dec 2021 09:09:09: 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 09:09:16: 5000000 INFO @ Sat, 11 Dec 2021 09:09:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.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 09:09:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:09:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:09:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:09:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:09:19: #1 total tags in treatment: 5476463 INFO @ Sat, 11 Dec 2021 09:09:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:09:19: #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 09:09:19: #1 tags after filtering in treatment: 5476459 INFO @ Sat, 11 Dec 2021 09:09:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:09:19: #1 finished! INFO @ Sat, 11 Dec 2021 09:09:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:09:20: #2 number of paired peaks: 618 WARNING @ Sat, 11 Dec 2021 09:09:20: Fewer paired peaks (618) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 618 pairs to build model! INFO @ Sat, 11 Dec 2021 09:09:20: start model_add_line... INFO @ Sat, 11 Dec 2021 09:09:20: start X-correlation... INFO @ Sat, 11 Dec 2021 09:09:20: end of X-cor INFO @ Sat, 11 Dec 2021 09:09:20: #2 finished! INFO @ Sat, 11 Dec 2021 09:09:20: #2 predicted fragment length is 60 bps INFO @ Sat, 11 Dec 2021 09:09:20: #2 alternative fragment length(s) may be 60 bps INFO @ Sat, 11 Dec 2021 09:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.05_model.r WARNING @ Sat, 11 Dec 2021 09:09:20: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:09:20: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sat, 11 Dec 2021 09:09:20: #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 09:09:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:09:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:09:23: 1000000 INFO @ Sat, 11 Dec 2021 09:09:29: 2000000 INFO @ Sat, 11 Dec 2021 09:09:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:09:35: 3000000 INFO @ Sat, 11 Dec 2021 09:09:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:09:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:09:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.05_summits.bed INFO @ Sat, 11 Dec 2021 09:09:36: Done! pass1 - making usageList (529 chroms): 1 millis pass2 - checking and writing primary data (1325 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:09:41: 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 09:09:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.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 09:09:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:09:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:09:48: 5000000 INFO @ Sat, 11 Dec 2021 09:09:52: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:09:52: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:09:52: #1 total tags in treatment: 5476463 INFO @ Sat, 11 Dec 2021 09:09:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:09:52: #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 09:09:52: #1 tags after filtering in treatment: 5476459 INFO @ Sat, 11 Dec 2021 09:09:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:09:52: #1 finished! INFO @ Sat, 11 Dec 2021 09:09:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:09:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:09:53: #2 number of paired peaks: 618 WARNING @ Sat, 11 Dec 2021 09:09:53: Fewer paired peaks (618) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 618 pairs to build model! INFO @ Sat, 11 Dec 2021 09:09:53: start model_add_line... INFO @ Sat, 11 Dec 2021 09:09:53: start X-correlation... INFO @ Sat, 11 Dec 2021 09:09:53: end of X-cor INFO @ Sat, 11 Dec 2021 09:09:53: #2 finished! INFO @ Sat, 11 Dec 2021 09:09:53: #2 predicted fragment length is 60 bps INFO @ Sat, 11 Dec 2021 09:09:53: #2 alternative fragment length(s) may be 60 bps INFO @ Sat, 11 Dec 2021 09:09:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.10_model.r WARNING @ Sat, 11 Dec 2021 09:09:53: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:09:53: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sat, 11 Dec 2021 09:09:53: #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 09:09:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:09:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:09:54: 1000000 INFO @ Sat, 11 Dec 2021 09:10:01: 2000000 INFO @ Sat, 11 Dec 2021 09:10:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:10:09: 3000000 INFO @ Sat, 11 Dec 2021 09:10:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:10:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.10_peaks.narrowPeak BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:10:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.10_summits.bed INFO @ Sat, 11 Dec 2021 09:10:09: Done! pass1 - making usageList (252 chroms): 1 millis pass2 - checking and writing primary data (522 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:10:16: 4000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:10:24: 5000000 INFO @ Sat, 11 Dec 2021 09:10:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:10:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:10:27: #1 total tags in treatment: 5476463 INFO @ Sat, 11 Dec 2021 09:10:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:10:27: #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 09:10:27: #1 tags after filtering in treatment: 5476459 INFO @ Sat, 11 Dec 2021 09:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:10:27: #1 finished! INFO @ Sat, 11 Dec 2021 09:10:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:10:28: #2 number of paired peaks: 618 WARNING @ Sat, 11 Dec 2021 09:10:28: Fewer paired peaks (618) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 618 pairs to build model! INFO @ Sat, 11 Dec 2021 09:10:28: start model_add_line... INFO @ Sat, 11 Dec 2021 09:10:28: start X-correlation... INFO @ Sat, 11 Dec 2021 09:10:28: end of X-cor INFO @ Sat, 11 Dec 2021 09:10:28: #2 finished! INFO @ Sat, 11 Dec 2021 09:10:28: #2 predicted fragment length is 60 bps INFO @ Sat, 11 Dec 2021 09:10:28: #2 alternative fragment length(s) may be 60 bps INFO @ Sat, 11 Dec 2021 09:10:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.20_model.r WARNING @ Sat, 11 Dec 2021 09:10:28: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:10:28: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sat, 11 Dec 2021 09:10:28: #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 09:10:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:10:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:10:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:10:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:10:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689092/SRX8689092.20_summits.bed INFO @ Sat, 11 Dec 2021 09:10:44: Done! pass1 - making usageList (119 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 5 millis CompletedMACS2peakCalling