Job ID = 14170939 SRX = SRX8689083 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: 00:02:36 8601543 reads; of these: 8601543 (100.00%) were unpaired; of these: 451475 (5.25%) aligned 0 times 5271810 (61.29%) aligned exactly 1 time 2878258 (33.46%) aligned >1 times 94.75% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 957807 / 8150068 = 0.1175 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 09:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.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 09:06:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:06:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:06:52: 1000000 INFO @ Sat, 11 Dec 2021 09:06:57: 2000000 INFO @ Sat, 11 Dec 2021 09:07:03: 3000000 INFO @ Sat, 11 Dec 2021 09:07:08: 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 09:07:14: 5000000 INFO @ Sat, 11 Dec 2021 09:07:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.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 09:07:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:07:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:07:20: 6000000 INFO @ Sat, 11 Dec 2021 09:07:22: 1000000 INFO @ Sat, 11 Dec 2021 09:07:26: 7000000 INFO @ Sat, 11 Dec 2021 09:07:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:07:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:07:27: #1 total tags in treatment: 7192261 INFO @ Sat, 11 Dec 2021 09:07:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:07:27: #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 09:07:28: #1 tags after filtering in treatment: 7192260 INFO @ Sat, 11 Dec 2021 09:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:07:28: #1 finished! INFO @ Sat, 11 Dec 2021 09:07:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:07:28: 2000000 INFO @ Sat, 11 Dec 2021 09:07:28: #2 number of paired peaks: 491 WARNING @ Sat, 11 Dec 2021 09:07:28: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Sat, 11 Dec 2021 09:07:28: start model_add_line... INFO @ Sat, 11 Dec 2021 09:07:28: start X-correlation... INFO @ Sat, 11 Dec 2021 09:07:28: end of X-cor INFO @ Sat, 11 Dec 2021 09:07:28: #2 finished! INFO @ Sat, 11 Dec 2021 09:07:28: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 09:07:28: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 09:07:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.05_model.r WARNING @ Sat, 11 Dec 2021 09:07:28: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:07:28: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 09:07:28: #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 09:07:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:07:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:07:34: 3000000 INFO @ Sat, 11 Dec 2021 09:07:39: 4000000 INFO @ Sat, 11 Dec 2021 09:07:43: #3 Call peaks for each chromosome... 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 09:07:45: 5000000 INFO @ Sat, 11 Dec 2021 09:07:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.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 09:07:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:07:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:07:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:07:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:07:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.05_summits.bed INFO @ Sat, 11 Dec 2021 09:07:50: Done! pass1 - making usageList (727 chroms): 2 millis pass2 - checking and writing primary data (2138 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:07:51: 6000000 INFO @ Sat, 11 Dec 2021 09:07:52: 1000000 INFO @ Sat, 11 Dec 2021 09:07:58: 7000000 INFO @ Sat, 11 Dec 2021 09:07:58: 2000000 INFO @ Sat, 11 Dec 2021 09:07:59: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:07:59: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:07:59: #1 total tags in treatment: 7192261 INFO @ Sat, 11 Dec 2021 09:07:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:07:59: #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 09:07:59: #1 tags after filtering in treatment: 7192260 INFO @ Sat, 11 Dec 2021 09:07:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:07:59: #1 finished! INFO @ Sat, 11 Dec 2021 09:07:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:07:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:08:00: #2 number of paired peaks: 491 WARNING @ Sat, 11 Dec 2021 09:08:00: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Sat, 11 Dec 2021 09:08:00: start model_add_line... INFO @ Sat, 11 Dec 2021 09:08:00: start X-correlation... INFO @ Sat, 11 Dec 2021 09:08:00: end of X-cor INFO @ Sat, 11 Dec 2021 09:08:00: #2 finished! INFO @ Sat, 11 Dec 2021 09:08:00: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 09:08:00: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 09:08:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.10_model.r WARNING @ Sat, 11 Dec 2021 09:08:00: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:08:00: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 09:08:00: #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 09:08:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:08:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:08:04: 3000000 INFO @ Sat, 11 Dec 2021 09:08:09: 4000000 INFO @ Sat, 11 Dec 2021 09:08:14: 5000000 INFO @ Sat, 11 Dec 2021 09:08:15: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:08:20: 6000000 INFO @ Sat, 11 Dec 2021 09:08:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:08:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:08:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.10_summits.bed INFO @ Sat, 11 Dec 2021 09:08:22: Done! pass1 - making usageList (381 chroms): 1 millis pass2 - checking and writing primary data (759 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:08:26: 7000000 INFO @ Sat, 11 Dec 2021 09:08:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:08:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:08:27: #1 total tags in treatment: 7192261 INFO @ Sat, 11 Dec 2021 09:08:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:08:27: #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 09:08:27: #1 tags after filtering in treatment: 7192260 INFO @ Sat, 11 Dec 2021 09:08:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:08:27: #1 finished! INFO @ Sat, 11 Dec 2021 09:08:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:08:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:08:28: #2 number of paired peaks: 491 WARNING @ Sat, 11 Dec 2021 09:08:28: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Sat, 11 Dec 2021 09:08:28: start model_add_line... INFO @ Sat, 11 Dec 2021 09:08:28: start X-correlation... INFO @ Sat, 11 Dec 2021 09:08:28: end of X-cor INFO @ Sat, 11 Dec 2021 09:08:28: #2 finished! INFO @ Sat, 11 Dec 2021 09:08:28: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 09:08:28: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 09:08:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.20_model.r WARNING @ Sat, 11 Dec 2021 09:08:28: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:08:28: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 09:08:28: #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 09:08:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:08:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:08:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:08:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:08:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:08:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689083/SRX8689083.20_summits.bed INFO @ Sat, 11 Dec 2021 09:08:50: Done! pass1 - making usageList (138 chroms): 2 millis pass2 - checking and writing primary data (291 records, 4 fields): 5 millis CompletedMACS2peakCalling