Job ID = 14168160 SRX = SRX8688983 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6448382 spots for SRR12174320/SRR12174320.sra Written 6448382 spots for SRR12174320/SRR12174320.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168960 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:17 6448382 reads; of these: 6448382 (100.00%) were unpaired; of these: 171182 (2.65%) aligned 0 times 4373602 (67.82%) aligned exactly 1 time 1903598 (29.52%) aligned >1 times 97.35% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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] 288361 / 6277200 = 0.0459 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 @ Fri, 10 Dec 2021 15:51:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.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 @ Fri, 10 Dec 2021 15:51:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:51:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:51:29: 1000000 INFO @ Fri, 10 Dec 2021 15:51:35: 2000000 INFO @ Fri, 10 Dec 2021 15:51:41: 3000000 INFO @ Fri, 10 Dec 2021 15:51:46: 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 @ Fri, 10 Dec 2021 15:51:52: 5000000 INFO @ Fri, 10 Dec 2021 15:51:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.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 @ Fri, 10 Dec 2021 15:51:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:51:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:51:59: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:51:59: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:51:59: #1 total tags in treatment: 5988839 INFO @ Fri, 10 Dec 2021 15:51:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:51:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:51:59: #1 tags after filtering in treatment: 5988839 INFO @ Fri, 10 Dec 2021 15:51:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:51:59: #1 finished! INFO @ Fri, 10 Dec 2021 15:51:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:51:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:51:59: #2 number of paired peaks: 449 WARNING @ Fri, 10 Dec 2021 15:51:59: Fewer paired peaks (449) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 449 pairs to build model! INFO @ Fri, 10 Dec 2021 15:51:59: start model_add_line... INFO @ Fri, 10 Dec 2021 15:51:59: start X-correlation... INFO @ Fri, 10 Dec 2021 15:51:59: end of X-cor INFO @ Fri, 10 Dec 2021 15:51:59: #2 finished! INFO @ Fri, 10 Dec 2021 15:51:59: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 15:51:59: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 15:51:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.05_model.r WARNING @ Fri, 10 Dec 2021 15:51:59: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:51:59: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 15:51:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:51:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:51:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:52:02: 1000000 INFO @ Fri, 10 Dec 2021 15:52:09: 2000000 INFO @ Fri, 10 Dec 2021 15:52:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:52:16: 3000000 INFO @ Fri, 10 Dec 2021 15:52:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:52:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:52:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.05_summits.bed INFO @ Fri, 10 Dec 2021 15:52:18: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1452 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 @ Fri, 10 Dec 2021 15:52:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.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 @ Fri, 10 Dec 2021 15:52:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:52:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:52:24: 4000000 INFO @ Fri, 10 Dec 2021 15:52:31: 1000000 INFO @ Fri, 10 Dec 2021 15:52:32: 5000000 INFO @ Fri, 10 Dec 2021 15:52:38: 2000000 INFO @ Fri, 10 Dec 2021 15:52:40: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:52:40: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:52:40: #1 total tags in treatment: 5988839 INFO @ Fri, 10 Dec 2021 15:52:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:52:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:52:40: #1 tags after filtering in treatment: 5988839 INFO @ Fri, 10 Dec 2021 15:52:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:52:40: #1 finished! INFO @ Fri, 10 Dec 2021 15:52:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:52:41: #2 number of paired peaks: 449 WARNING @ Fri, 10 Dec 2021 15:52:41: Fewer paired peaks (449) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 449 pairs to build model! INFO @ Fri, 10 Dec 2021 15:52:41: start model_add_line... INFO @ Fri, 10 Dec 2021 15:52:41: start X-correlation... INFO @ Fri, 10 Dec 2021 15:52:41: end of X-cor INFO @ Fri, 10 Dec 2021 15:52:41: #2 finished! INFO @ Fri, 10 Dec 2021 15:52:41: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 15:52:41: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 15:52:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.10_model.r WARNING @ Fri, 10 Dec 2021 15:52:41: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:52:41: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 15:52:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:52:41: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:52:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:52:45: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:52:51: 4000000 INFO @ Fri, 10 Dec 2021 15:52:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:52:57: 5000000 INFO @ Fri, 10 Dec 2021 15:52:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:52:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:52:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.10_summits.bed INFO @ Fri, 10 Dec 2021 15:52:59: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (1184 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:53:03: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:53:03: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:53:03: #1 total tags in treatment: 5988839 INFO @ Fri, 10 Dec 2021 15:53:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:53:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:53:03: #1 tags after filtering in treatment: 5988839 INFO @ Fri, 10 Dec 2021 15:53:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:53:03: #1 finished! INFO @ Fri, 10 Dec 2021 15:53:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:53:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:53:03: #2 number of paired peaks: 449 WARNING @ Fri, 10 Dec 2021 15:53:03: Fewer paired peaks (449) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 449 pairs to build model! INFO @ Fri, 10 Dec 2021 15:53:03: start model_add_line... INFO @ Fri, 10 Dec 2021 15:53:03: start X-correlation... INFO @ Fri, 10 Dec 2021 15:53:03: end of X-cor INFO @ Fri, 10 Dec 2021 15:53:03: #2 finished! INFO @ Fri, 10 Dec 2021 15:53:03: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 15:53:03: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 15:53:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.20_model.r WARNING @ Fri, 10 Dec 2021 15:53:03: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:53:03: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 15:53:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:53:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:53:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:53:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:53:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:53:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:53:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688983/SRX8688983.20_summits.bed INFO @ Fri, 10 Dec 2021 15:53:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (831 records, 4 fields): 2 millis CompletedMACS2peakCalling