Job ID = 14170391 SRX = SRX8689012 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8352075 spots for SRR12174301/SRR12174301.sra Written 8352075 spots for SRR12174301/SRR12174301.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170801 ("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: 00:03:49 8352075 reads; of these: 8352075 (100.00%) were unpaired; of these: 352908 (4.23%) aligned 0 times 5829325 (69.79%) aligned exactly 1 time 2169842 (25.98%) aligned >1 times 95.77% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 1445057 / 7999167 = 0.1807 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 06:46:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.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 06:46:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:46:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:46:49: 1000000 INFO @ Sat, 11 Dec 2021 06:46:58: 2000000 INFO @ Sat, 11 Dec 2021 06:47:06: 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 06:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.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 06:47:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:47:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:47:15: 4000000 INFO @ Sat, 11 Dec 2021 06:47:19: 1000000 INFO @ Sat, 11 Dec 2021 06:47:24: 5000000 INFO @ Sat, 11 Dec 2021 06:47:27: 2000000 INFO @ Sat, 11 Dec 2021 06:47:33: 6000000 INFO @ Sat, 11 Dec 2021 06:47:36: 3000000 INFO @ Sat, 11 Dec 2021 06:47:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:38: #1 total tags in treatment: 6554110 INFO @ Sat, 11 Dec 2021 06:47:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:38: #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 06:47:38: #1 tags after filtering in treatment: 6554110 INFO @ Sat, 11 Dec 2021 06:47:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:38: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:38: #2 looking for paired plus/minus strand peaks... 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 06:47:38: #2 number of paired peaks: 361 WARNING @ Sat, 11 Dec 2021 06:47:38: 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 06:47:38: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:39: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:39: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:39: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:39: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 06:47:39: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 06:47:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.05_model.r WARNING @ Sat, 11 Dec 2021 06:47:39: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:47:39: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 06:47:39: #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 06:47:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:47:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.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 06:47:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:47:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:47:44: 4000000 INFO @ Sat, 11 Dec 2021 06:47:50: 1000000 INFO @ Sat, 11 Dec 2021 06:47:52: 5000000 INFO @ Sat, 11 Dec 2021 06:47:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:47:59: 2000000 INFO @ Sat, 11 Dec 2021 06:48:00: 6000000 INFO @ Sat, 11 Dec 2021 06:48:04: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:48:04: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:48:04: #1 total tags in treatment: 6554110 INFO @ Sat, 11 Dec 2021 06:48:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:48:04: #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 06:48:05: #1 tags after filtering in treatment: 6554110 INFO @ Sat, 11 Dec 2021 06:48:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:48:05: #1 finished! INFO @ Sat, 11 Dec 2021 06:48:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:48:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:48:05: #2 number of paired peaks: 361 WARNING @ Sat, 11 Dec 2021 06:48:05: 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 06:48:05: start model_add_line... INFO @ Sat, 11 Dec 2021 06:48:05: start X-correlation... INFO @ Sat, 11 Dec 2021 06:48:05: end of X-cor INFO @ Sat, 11 Dec 2021 06:48:05: #2 finished! INFO @ Sat, 11 Dec 2021 06:48:05: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 06:48:05: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 06:48:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.10_model.r WARNING @ Sat, 11 Dec 2021 06:48:05: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:48:05: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 06:48:05: #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 06:48:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:48:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:48:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:48:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:48:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.05_summits.bed INFO @ Sat, 11 Dec 2021 06:48:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1355 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:48:07: 3000000 INFO @ Sat, 11 Dec 2021 06:48:16: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:48:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:48:24: 5000000 INFO @ Sat, 11 Dec 2021 06:48:33: 6000000 INFO @ Sat, 11 Dec 2021 06:48:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:48:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.10_summits.bed INFO @ Sat, 11 Dec 2021 06:48:34: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1117 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:48:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:48:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:48:38: #1 total tags in treatment: 6554110 INFO @ Sat, 11 Dec 2021 06:48:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:48:38: #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 06:48:38: #1 tags after filtering in treatment: 6554110 INFO @ Sat, 11 Dec 2021 06:48:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:48:38: #1 finished! INFO @ Sat, 11 Dec 2021 06:48:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:48:39: #2 number of paired peaks: 361 WARNING @ Sat, 11 Dec 2021 06:48:39: 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 06:48:39: start model_add_line... INFO @ Sat, 11 Dec 2021 06:48:39: start X-correlation... INFO @ Sat, 11 Dec 2021 06:48:39: end of X-cor INFO @ Sat, 11 Dec 2021 06:48:39: #2 finished! INFO @ Sat, 11 Dec 2021 06:48:39: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 06:48:39: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 06:48:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.20_model.r WARNING @ Sat, 11 Dec 2021 06:48:39: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:48:39: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 06:48:39: #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 06:48:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:48:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:48:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:49:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:49:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:49:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689012/SRX8689012.20_summits.bed INFO @ Sat, 11 Dec 2021 06:49:07: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (799 records, 4 fields): 4 millis CompletedMACS2peakCalling