Job ID = 12266683 SRX = SRX8622118 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20506857 spots for SRR12096678/SRR12096678.sra Written 20506857 spots for SRR12096678/SRR12096678.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267215 ("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: 00:36:40 20506857 reads; of these: 20506857 (100.00%) were paired; of these: 14200729 (69.25%) aligned concordantly 0 times 4065277 (19.82%) aligned concordantly exactly 1 time 2240851 (10.93%) aligned concordantly >1 times ---- 14200729 pairs aligned concordantly 0 times; of these: 1465629 (10.32%) aligned discordantly 1 time ---- 12735100 pairs aligned 0 times concordantly or discordantly; of these: 25470200 mates make up the pairs; of these: 22783019 (89.45%) aligned 0 times 858627 (3.37%) aligned exactly 1 time 1828554 (7.18%) aligned >1 times 44.45% overall alignment rate Time searching: 00:36:40 Overall time: 00:36:40 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 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1718588 / 7724901 = 0.2225 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:54:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.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, 03 Apr 2021 09:54:05: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:54:05: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:54:15: 1000000 INFO @ Sat, 03 Apr 2021 09:54:25: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:54:34: 3000000 INFO @ Sat, 03 Apr 2021 09:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.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, 03 Apr 2021 09:54:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:54:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:54:45: 4000000 INFO @ Sat, 03 Apr 2021 09:54:46: 1000000 INFO @ Sat, 03 Apr 2021 09:54:56: 5000000 INFO @ Sat, 03 Apr 2021 09:54:57: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:55:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.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, 03 Apr 2021 09:55:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:55:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:55:07: 6000000 INFO @ Sat, 03 Apr 2021 09:55:08: 3000000 INFO @ Sat, 03 Apr 2021 09:55:18: 1000000 INFO @ Sat, 03 Apr 2021 09:55:19: 7000000 INFO @ Sat, 03 Apr 2021 09:55:20: 4000000 INFO @ Sat, 03 Apr 2021 09:55:31: 8000000 INFO @ Sat, 03 Apr 2021 09:55:31: 2000000 INFO @ Sat, 03 Apr 2021 09:55:32: 5000000 INFO @ Sat, 03 Apr 2021 09:55:43: 9000000 INFO @ Sat, 03 Apr 2021 09:55:43: 3000000 INFO @ Sat, 03 Apr 2021 09:55:44: 6000000 INFO @ Sat, 03 Apr 2021 09:55:54: 10000000 INFO @ Sat, 03 Apr 2021 09:55:56: 4000000 INFO @ Sat, 03 Apr 2021 09:55:56: 7000000 INFO @ Sat, 03 Apr 2021 09:56:06: 11000000 INFO @ Sat, 03 Apr 2021 09:56:08: 8000000 INFO @ Sat, 03 Apr 2021 09:56:08: 5000000 INFO @ Sat, 03 Apr 2021 09:56:17: 12000000 INFO @ Sat, 03 Apr 2021 09:56:19: 9000000 INFO @ Sat, 03 Apr 2021 09:56:21: 6000000 INFO @ Sat, 03 Apr 2021 09:56:29: 13000000 INFO @ Sat, 03 Apr 2021 09:56:31: 10000000 INFO @ Sat, 03 Apr 2021 09:56:33: 7000000 INFO @ Sat, 03 Apr 2021 09:56:41: 14000000 INFO @ Sat, 03 Apr 2021 09:56:42: 11000000 INFO @ Sat, 03 Apr 2021 09:56:45: 8000000 INFO @ Sat, 03 Apr 2021 09:56:50: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:56:50: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:56:50: #1 total tags in treatment: 4734750 INFO @ Sat, 03 Apr 2021 09:56:50: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:56:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:56:50: #1 tags after filtering in treatment: 3886701 INFO @ Sat, 03 Apr 2021 09:56:50: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 09:56:50: #1 finished! INFO @ Sat, 03 Apr 2021 09:56:50: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:56:50: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:56:50: #2 number of paired peaks: 991 WARNING @ Sat, 03 Apr 2021 09:56:50: Fewer paired peaks (991) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 991 pairs to build model! INFO @ Sat, 03 Apr 2021 09:56:50: start model_add_line... INFO @ Sat, 03 Apr 2021 09:56:50: start X-correlation... INFO @ Sat, 03 Apr 2021 09:56:50: end of X-cor INFO @ Sat, 03 Apr 2021 09:56:50: #2 finished! INFO @ Sat, 03 Apr 2021 09:56:50: #2 predicted fragment length is 206 bps INFO @ Sat, 03 Apr 2021 09:56:50: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 03 Apr 2021 09:56:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.05_model.r WARNING @ Sat, 03 Apr 2021 09:56:50: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:56:50: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Sat, 03 Apr 2021 09:56:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:56:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:56:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:56:53: 12000000 INFO @ Sat, 03 Apr 2021 09:56:58: 9000000 INFO @ Sat, 03 Apr 2021 09:57:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:57:05: 13000000 INFO @ Sat, 03 Apr 2021 09:57:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:57:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:57:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.05_summits.bed INFO @ Sat, 03 Apr 2021 09:57:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2368 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:57:10: 10000000 INFO @ Sat, 03 Apr 2021 09:57:17: 14000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:57:22: 11000000 INFO @ Sat, 03 Apr 2021 09:57:26: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:57:26: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:57:26: #1 total tags in treatment: 4734750 INFO @ Sat, 03 Apr 2021 09:57:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:57:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:57:26: #1 tags after filtering in treatment: 3886701 INFO @ Sat, 03 Apr 2021 09:57:26: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 09:57:26: #1 finished! INFO @ Sat, 03 Apr 2021 09:57:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:57:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:57:26: #2 number of paired peaks: 991 WARNING @ Sat, 03 Apr 2021 09:57:26: Fewer paired peaks (991) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 991 pairs to build model! INFO @ Sat, 03 Apr 2021 09:57:26: start model_add_line... INFO @ Sat, 03 Apr 2021 09:57:27: start X-correlation... INFO @ Sat, 03 Apr 2021 09:57:27: end of X-cor INFO @ Sat, 03 Apr 2021 09:57:27: #2 finished! INFO @ Sat, 03 Apr 2021 09:57:27: #2 predicted fragment length is 206 bps INFO @ Sat, 03 Apr 2021 09:57:27: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 03 Apr 2021 09:57:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.10_model.r WARNING @ Sat, 03 Apr 2021 09:57:27: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:57:27: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Sat, 03 Apr 2021 09:57:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:57:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:57:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:57:33: 12000000 INFO @ Sat, 03 Apr 2021 09:57:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:57:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:57:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:57:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.10_summits.bed INFO @ Sat, 03 Apr 2021 09:57:43: Done! INFO @ Sat, 03 Apr 2021 09:57:44: 13000000 pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (926 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:57:55: 14000000 INFO @ Sat, 03 Apr 2021 09:58:03: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:58:03: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:58:03: #1 total tags in treatment: 4734750 INFO @ Sat, 03 Apr 2021 09:58:03: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:58:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:58:03: #1 tags after filtering in treatment: 3886701 INFO @ Sat, 03 Apr 2021 09:58:03: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 09:58:03: #1 finished! INFO @ Sat, 03 Apr 2021 09:58:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:58:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:58:04: #2 number of paired peaks: 991 WARNING @ Sat, 03 Apr 2021 09:58:04: Fewer paired peaks (991) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 991 pairs to build model! INFO @ Sat, 03 Apr 2021 09:58:04: start model_add_line... INFO @ Sat, 03 Apr 2021 09:58:04: start X-correlation... INFO @ Sat, 03 Apr 2021 09:58:04: end of X-cor INFO @ Sat, 03 Apr 2021 09:58:04: #2 finished! INFO @ Sat, 03 Apr 2021 09:58:04: #2 predicted fragment length is 206 bps INFO @ Sat, 03 Apr 2021 09:58:04: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 03 Apr 2021 09:58:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.20_model.r WARNING @ Sat, 03 Apr 2021 09:58:04: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:58:04: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Sat, 03 Apr 2021 09:58:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:58:04: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:58:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:58:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:58:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:58:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:58:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622118/SRX8622118.20_summits.bed INFO @ Sat, 03 Apr 2021 09:58:19: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (279 records, 4 fields): 2 millis CompletedMACS2peakCalling