Job ID = 14168157 SRX = SRX8688980 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15362295 spots for SRR12174349/SRR12174349.sra Written 15362295 spots for SRR12174349/SRR12174349.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168972 ("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: 00:05:53 15362295 reads; of these: 15362295 (100.00%) were unpaired; of these: 451684 (2.94%) aligned 0 times 9861759 (64.19%) aligned exactly 1 time 5048852 (32.87%) aligned >1 times 97.06% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1473269 / 14910611 = 0.0988 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 15:55:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.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 15:55:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:55:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:55:58: 1000000 INFO @ Fri, 10 Dec 2021 15:56:03: 2000000 INFO @ Fri, 10 Dec 2021 15:56:09: 3000000 INFO @ Fri, 10 Dec 2021 15:56:14: 4000000 INFO @ Fri, 10 Dec 2021 15:56:20: 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 @ Fri, 10 Dec 2021 15:56:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.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 15:56:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:56:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:56:26: 6000000 INFO @ Fri, 10 Dec 2021 15:56:28: 1000000 INFO @ Fri, 10 Dec 2021 15:56:32: 7000000 INFO @ Fri, 10 Dec 2021 15:56:35: 2000000 INFO @ Fri, 10 Dec 2021 15:56:39: 8000000 INFO @ Fri, 10 Dec 2021 15:56:41: 3000000 INFO @ Fri, 10 Dec 2021 15:56:45: 9000000 INFO @ Fri, 10 Dec 2021 15:56:48: 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 @ Fri, 10 Dec 2021 15:56:52: 10000000 INFO @ Fri, 10 Dec 2021 15:56:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.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 15:56:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:56:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:56:54: 5000000 INFO @ Fri, 10 Dec 2021 15:56:58: 11000000 INFO @ Fri, 10 Dec 2021 15:56:58: 1000000 INFO @ Fri, 10 Dec 2021 15:57:01: 6000000 INFO @ Fri, 10 Dec 2021 15:57:05: 12000000 INFO @ Fri, 10 Dec 2021 15:57:05: 2000000 INFO @ Fri, 10 Dec 2021 15:57:07: 7000000 INFO @ Fri, 10 Dec 2021 15:57:11: 13000000 INFO @ Fri, 10 Dec 2021 15:57:11: 3000000 INFO @ Fri, 10 Dec 2021 15:57:14: 8000000 INFO @ Fri, 10 Dec 2021 15:57:14: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:57:14: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:57:14: #1 total tags in treatment: 13437342 INFO @ Fri, 10 Dec 2021 15:57:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:57:14: #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 15:57:14: #1 tags after filtering in treatment: 13437342 INFO @ Fri, 10 Dec 2021 15:57:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:57:14: #1 finished! INFO @ Fri, 10 Dec 2021 15:57:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:57:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:57:15: #2 number of paired peaks: 315 WARNING @ Fri, 10 Dec 2021 15:57:15: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 10 Dec 2021 15:57:15: start model_add_line... INFO @ Fri, 10 Dec 2021 15:57:15: start X-correlation... INFO @ Fri, 10 Dec 2021 15:57:15: end of X-cor INFO @ Fri, 10 Dec 2021 15:57:15: #2 finished! INFO @ Fri, 10 Dec 2021 15:57:15: #2 predicted fragment length is 47 bps INFO @ Fri, 10 Dec 2021 15:57:15: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 10 Dec 2021 15:57:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.05_model.r WARNING @ Fri, 10 Dec 2021 15:57:15: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:57:15: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 10 Dec 2021 15:57:15: #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 15:57:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:57:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:57:18: 4000000 INFO @ Fri, 10 Dec 2021 15:57:20: 9000000 INFO @ Fri, 10 Dec 2021 15:57:24: 5000000 INFO @ Fri, 10 Dec 2021 15:57:26: 10000000 INFO @ Fri, 10 Dec 2021 15:57:30: 6000000 INFO @ Fri, 10 Dec 2021 15:57:33: 11000000 INFO @ Fri, 10 Dec 2021 15:57:37: 7000000 INFO @ Fri, 10 Dec 2021 15:57:39: 12000000 INFO @ Fri, 10 Dec 2021 15:57:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:57:43: 8000000 INFO @ Fri, 10 Dec 2021 15:57:46: 13000000 INFO @ Fri, 10 Dec 2021 15:57:48: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:57:48: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:57:48: #1 total tags in treatment: 13437342 INFO @ Fri, 10 Dec 2021 15:57:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:57:48: #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 15:57:49: #1 tags after filtering in treatment: 13437342 INFO @ Fri, 10 Dec 2021 15:57:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:57:49: #1 finished! INFO @ Fri, 10 Dec 2021 15:57:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:57:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:57:49: 9000000 INFO @ Fri, 10 Dec 2021 15:57:50: #2 number of paired peaks: 315 WARNING @ Fri, 10 Dec 2021 15:57:50: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 10 Dec 2021 15:57:50: start model_add_line... INFO @ Fri, 10 Dec 2021 15:57:50: start X-correlation... INFO @ Fri, 10 Dec 2021 15:57:50: end of X-cor INFO @ Fri, 10 Dec 2021 15:57:50: #2 finished! INFO @ Fri, 10 Dec 2021 15:57:50: #2 predicted fragment length is 47 bps INFO @ Fri, 10 Dec 2021 15:57:50: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 10 Dec 2021 15:57:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.10_model.r WARNING @ Fri, 10 Dec 2021 15:57:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:57:50: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 10 Dec 2021 15:57:50: #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 15:57:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:57:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:57:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:57:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:57:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.05_summits.bed INFO @ Fri, 10 Dec 2021 15:57:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2450 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:57:55: 10000000 INFO @ Fri, 10 Dec 2021 15:58:01: 11000000 INFO @ Fri, 10 Dec 2021 15:58:06: 12000000 INFO @ Fri, 10 Dec 2021 15:58:12: 13000000 INFO @ Fri, 10 Dec 2021 15:58:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:58:14: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:58:14: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:58:14: #1 total tags in treatment: 13437342 INFO @ Fri, 10 Dec 2021 15:58:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:58:14: #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 15:58:15: #1 tags after filtering in treatment: 13437342 INFO @ Fri, 10 Dec 2021 15:58:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:58:15: #1 finished! INFO @ Fri, 10 Dec 2021 15:58:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:58:16: #2 number of paired peaks: 315 WARNING @ Fri, 10 Dec 2021 15:58:16: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 10 Dec 2021 15:58:16: start model_add_line... INFO @ Fri, 10 Dec 2021 15:58:16: start X-correlation... INFO @ Fri, 10 Dec 2021 15:58:16: end of X-cor INFO @ Fri, 10 Dec 2021 15:58:16: #2 finished! INFO @ Fri, 10 Dec 2021 15:58:16: #2 predicted fragment length is 47 bps INFO @ Fri, 10 Dec 2021 15:58:16: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 10 Dec 2021 15:58:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.20_model.r WARNING @ Fri, 10 Dec 2021 15:58:16: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:58:16: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 10 Dec 2021 15:58:16: #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 15:58:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:58:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:58:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:58:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.10_summits.bed INFO @ Fri, 10 Dec 2021 15:58:27: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1481 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:58:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:58:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:58:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:58:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688980/SRX8688980.20_summits.bed INFO @ Fri, 10 Dec 2021 15:58:53: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (1064 records, 4 fields): 3 millis CompletedMACS2peakCalling