Job ID = 14170516 SRX = SRX8689074 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8063817 spots for SRR12174307/SRR12174307.sra Written 8063817 spots for SRR12174307/SRR12174307.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170923 ("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: 00:03:01 8063817 reads; of these: 8063817 (100.00%) were unpaired; of these: 582923 (7.23%) aligned 0 times 5391819 (66.86%) aligned exactly 1 time 2089075 (25.91%) aligned >1 times 92.77% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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] 351554 / 7480894 = 0.0470 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 07:08:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.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 07:08:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:08:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:08:35: 1000000 INFO @ Sat, 11 Dec 2021 07:08:42: 2000000 INFO @ Sat, 11 Dec 2021 07:08:50: 3000000 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 07:08:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.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 07:08:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:08:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:08:57: 4000000 INFO @ Sat, 11 Dec 2021 07:09:02: 1000000 INFO @ Sat, 11 Dec 2021 07:09:04: 5000000 INFO @ Sat, 11 Dec 2021 07:09:09: 2000000 INFO @ Sat, 11 Dec 2021 07:09:11: 6000000 INFO @ Sat, 11 Dec 2021 07:09:15: 3000000 INFO @ Sat, 11 Dec 2021 07:09:19: 7000000 INFO @ Sat, 11 Dec 2021 07:09:20: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:09:20: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:09:20: #1 total tags in treatment: 7129340 INFO @ Sat, 11 Dec 2021 07:09:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:09:20: #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 07:09:20: #1 tags after filtering in treatment: 7129340 INFO @ Sat, 11 Dec 2021 07:09:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:09:20: #1 finished! INFO @ Sat, 11 Dec 2021 07:09:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:09:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:09:20: #2 number of paired peaks: 195 WARNING @ Sat, 11 Dec 2021 07:09:20: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 11 Dec 2021 07:09:20: start model_add_line... INFO @ Sat, 11 Dec 2021 07:09:20: start X-correlation... INFO @ Sat, 11 Dec 2021 07:09:20: end of X-cor INFO @ Sat, 11 Dec 2021 07:09:20: #2 finished! INFO @ Sat, 11 Dec 2021 07:09:20: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 07:09:20: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 11 Dec 2021 07:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.05_model.r WARNING @ Sat, 11 Dec 2021 07:09:20: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:09:20: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 11 Dec 2021 07:09:20: #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 07:09:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:09:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:09:21: 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 07:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.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 07:09:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:09:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:09:27: 5000000 INFO @ Sat, 11 Dec 2021 07:09:33: 1000000 INFO @ Sat, 11 Dec 2021 07:09:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:09:34: 6000000 INFO @ Sat, 11 Dec 2021 07:09:40: 2000000 INFO @ Sat, 11 Dec 2021 07:09:41: 7000000 INFO @ Sat, 11 Dec 2021 07:09:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:09:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:09:41: #1 total tags in treatment: 7129340 INFO @ Sat, 11 Dec 2021 07:09:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:09:41: #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 07:09:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:09:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:09:42: #1 tags after filtering in treatment: 7129340 INFO @ Sat, 11 Dec 2021 07:09:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:09:42: #1 finished! INFO @ Sat, 11 Dec 2021 07:09:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:09:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:09:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.05_summits.bed INFO @ Sat, 11 Dec 2021 07:09:42: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1116 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:09:42: #2 number of paired peaks: 195 WARNING @ Sat, 11 Dec 2021 07:09:42: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 11 Dec 2021 07:09:42: start model_add_line... INFO @ Sat, 11 Dec 2021 07:09:42: start X-correlation... INFO @ Sat, 11 Dec 2021 07:09:42: end of X-cor INFO @ Sat, 11 Dec 2021 07:09:42: #2 finished! INFO @ Sat, 11 Dec 2021 07:09:42: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 07:09:42: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 11 Dec 2021 07:09:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.10_model.r WARNING @ Sat, 11 Dec 2021 07:09:42: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:09:42: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 11 Dec 2021 07:09:42: #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 07:09:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:09:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:09:46: 3000000 INFO @ Sat, 11 Dec 2021 07:09:52: 4000000 INFO @ Sat, 11 Dec 2021 07:09:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:09:58: 5000000 INFO @ Sat, 11 Dec 2021 07:10:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:10:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:10:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.10_summits.bed INFO @ Sat, 11 Dec 2021 07:10:03: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (918 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:10:04: 6000000 INFO @ Sat, 11 Dec 2021 07:10:10: 7000000 INFO @ Sat, 11 Dec 2021 07:10:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:10:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:10:11: #1 total tags in treatment: 7129340 INFO @ Sat, 11 Dec 2021 07:10:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:10:11: #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 07:10:11: #1 tags after filtering in treatment: 7129340 INFO @ Sat, 11 Dec 2021 07:10:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:10:11: #1 finished! INFO @ Sat, 11 Dec 2021 07:10:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:10:11: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:10:12: #2 number of paired peaks: 195 WARNING @ Sat, 11 Dec 2021 07:10:12: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 11 Dec 2021 07:10:12: start model_add_line... INFO @ Sat, 11 Dec 2021 07:10:12: start X-correlation... INFO @ Sat, 11 Dec 2021 07:10:12: end of X-cor INFO @ Sat, 11 Dec 2021 07:10:12: #2 finished! INFO @ Sat, 11 Dec 2021 07:10:12: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 07:10:12: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 11 Dec 2021 07:10:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.20_model.r WARNING @ Sat, 11 Dec 2021 07:10:12: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:10:12: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 11 Dec 2021 07:10:12: #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 07:10:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:10:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:10:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:10:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:10:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:10:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689074/SRX8689074.20_summits.bed INFO @ Sat, 11 Dec 2021 07:10:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (663 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。