Job ID = 14170535 SRX = SRX8689081 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6889307 spots for SRR12174249/SRR12174249.sra Written 6889307 spots for SRR12174249/SRR12174249.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170936 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:46 6889307 reads; of these: 6889307 (100.00%) were unpaired; of these: 170098 (2.47%) aligned 0 times 4958617 (71.98%) aligned exactly 1 time 1760592 (25.56%) aligned >1 times 97.53% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 307502 / 6719209 = 0.0458 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 07:12:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.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 07:12:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:12:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:12:26: 1000000 INFO @ Sat, 11 Dec 2021 07:12:32: 2000000 INFO @ Sat, 11 Dec 2021 07:12:37: 3000000 INFO @ Sat, 11 Dec 2021 07:12:42: 4000000 INFO @ Sat, 11 Dec 2021 07:12:48: 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 @ Sat, 11 Dec 2021 07:12:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.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 07:12:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:12:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:12:54: 6000000 INFO @ Sat, 11 Dec 2021 07:12:56: 1000000 INFO @ Sat, 11 Dec 2021 07:12:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:12:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:12:56: #1 total tags in treatment: 6411707 INFO @ Sat, 11 Dec 2021 07:12:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:12:56: #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 07:12:56: #1 tags after filtering in treatment: 6411707 INFO @ Sat, 11 Dec 2021 07:12:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:12:56: #1 finished! INFO @ Sat, 11 Dec 2021 07:12:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:12:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:12:57: #2 number of paired peaks: 361 WARNING @ Sat, 11 Dec 2021 07:12:57: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Sat, 11 Dec 2021 07:12:57: start model_add_line... INFO @ Sat, 11 Dec 2021 07:12:57: start X-correlation... INFO @ Sat, 11 Dec 2021 07:12:57: end of X-cor INFO @ Sat, 11 Dec 2021 07:12:57: #2 finished! INFO @ Sat, 11 Dec 2021 07:12:57: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:12:57: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 07:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.05_model.r WARNING @ Sat, 11 Dec 2021 07:12:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:12:57: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 07:12:57: #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 07:12:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:12:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:13:02: 2000000 INFO @ Sat, 11 Dec 2021 07:13:07: 3000000 INFO @ Sat, 11 Dec 2021 07:13:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:13:13: 4000000 INFO @ Sat, 11 Dec 2021 07:13:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:13:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:13:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.05_summits.bed INFO @ Sat, 11 Dec 2021 07:13:16: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1366 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 07:13:18: 5000000 INFO @ Sat, 11 Dec 2021 07:13:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.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 07:13:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:13:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:13:24: 6000000 INFO @ Sat, 11 Dec 2021 07:13:26: 1000000 INFO @ Sat, 11 Dec 2021 07:13:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:13:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:13:27: #1 total tags in treatment: 6411707 INFO @ Sat, 11 Dec 2021 07:13:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:13:27: #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 07:13:27: #1 tags after filtering in treatment: 6411707 INFO @ Sat, 11 Dec 2021 07:13:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:13:27: #1 finished! INFO @ Sat, 11 Dec 2021 07:13:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:13:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:13:27: #2 number of paired peaks: 361 WARNING @ Sat, 11 Dec 2021 07:13:27: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Sat, 11 Dec 2021 07:13:27: start model_add_line... INFO @ Sat, 11 Dec 2021 07:13:27: start X-correlation... INFO @ Sat, 11 Dec 2021 07:13:27: end of X-cor INFO @ Sat, 11 Dec 2021 07:13:27: #2 finished! INFO @ Sat, 11 Dec 2021 07:13:27: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:13:27: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 07:13:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.10_model.r WARNING @ Sat, 11 Dec 2021 07:13:27: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:13:27: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 07:13:27: #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 07:13:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:13:32: 2000000 INFO @ Sat, 11 Dec 2021 07:13:38: 3000000 INFO @ Sat, 11 Dec 2021 07:13:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:13:43: 4000000 INFO @ Sat, 11 Dec 2021 07:13:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:13:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:13:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.10_summits.bed INFO @ Sat, 11 Dec 2021 07:13:48: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1159 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:13:49: 5000000 INFO @ Sat, 11 Dec 2021 07:13:54: 6000000 INFO @ Sat, 11 Dec 2021 07:13:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:13:57: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:13:57: #1 total tags in treatment: 6411707 INFO @ Sat, 11 Dec 2021 07:13:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:13:57: #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 07:13:57: #1 tags after filtering in treatment: 6411707 INFO @ Sat, 11 Dec 2021 07:13:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:13:57: #1 finished! INFO @ Sat, 11 Dec 2021 07:13:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:13:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:13:57: #2 number of paired peaks: 361 WARNING @ Sat, 11 Dec 2021 07:13:57: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Sat, 11 Dec 2021 07:13:57: start model_add_line... INFO @ Sat, 11 Dec 2021 07:13:57: start X-correlation... INFO @ Sat, 11 Dec 2021 07:13:57: end of X-cor INFO @ Sat, 11 Dec 2021 07:13:57: #2 finished! INFO @ Sat, 11 Dec 2021 07:13:57: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:13:57: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 07:13:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.20_model.r WARNING @ Sat, 11 Dec 2021 07:13:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:13:57: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 07:13:57: #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 07:13:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:13:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:14:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:14:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:14:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:14:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689081/SRX8689081.20_summits.bed INFO @ Sat, 11 Dec 2021 07:14:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (814 records, 4 fields): 2 millis CompletedMACS2peakCalling