Job ID = 16437472 SRX = ERX5847866 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T03:38:36 prefetch.2.10.7: 1) Downloading 'ERR6212876'... 2022-08-02T03:38:36 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T03:39:09 prefetch.2.10.7: HTTPS download succeed 2022-08-02T03:39:10 prefetch.2.10.7: 'ERR6212876' is valid 2022-08-02T03:39:10 prefetch.2.10.7: 1) 'ERR6212876' was downloaded successfully 2022-08-02T03:39:10 prefetch.2.10.7: 'ERR6212876' has 0 unresolved dependencies Read 8092814 spots for ERR6212876/ERR6212876.sra Written 8092814 spots for ERR6212876/ERR6212876.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437603 ("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: 00:10:20 8092814 reads; of these: 8092814 (100.00%) were paired; of these: 2300320 (28.42%) aligned concordantly 0 times 3720668 (45.97%) aligned concordantly exactly 1 time 2071826 (25.60%) aligned concordantly >1 times ---- 2300320 pairs aligned concordantly 0 times; of these: 12766 (0.55%) aligned discordantly 1 time ---- 2287554 pairs aligned 0 times concordantly or discordantly; of these: 4575108 mates make up the pairs; of these: 3708537 (81.06%) aligned 0 times 535809 (11.71%) aligned exactly 1 time 330762 (7.23%) aligned >1 times 77.09% overall alignment rate Time searching: 00:10:21 Overall time: 00:10:21 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_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] 176732 / 5801522 = 0.0305 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:54:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.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 @ Tue, 02 Aug 2022 12:54:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:54:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:54:54: 1000000 INFO @ Tue, 02 Aug 2022 12:55:00: 2000000 INFO @ Tue, 02 Aug 2022 12:55:06: 3000000 INFO @ Tue, 02 Aug 2022 12:55:12: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:55:18: 5000000 INFO @ Tue, 02 Aug 2022 12:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.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 @ Tue, 02 Aug 2022 12:55:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:55:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:55:24: 6000000 INFO @ Tue, 02 Aug 2022 12:55:24: 1000000 INFO @ Tue, 02 Aug 2022 12:55:30: 7000000 INFO @ Tue, 02 Aug 2022 12:55:31: 2000000 INFO @ Tue, 02 Aug 2022 12:55:36: 8000000 INFO @ Tue, 02 Aug 2022 12:55:37: 3000000 INFO @ Tue, 02 Aug 2022 12:55:43: 9000000 INFO @ Tue, 02 Aug 2022 12:55:43: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.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 @ Tue, 02 Aug 2022 12:55:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:55:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:55:49: 5000000 INFO @ Tue, 02 Aug 2022 12:55:49: 10000000 INFO @ Tue, 02 Aug 2022 12:55:53: 1000000 INFO @ Tue, 02 Aug 2022 12:55:55: 6000000 INFO @ Tue, 02 Aug 2022 12:55:56: 11000000 INFO @ Tue, 02 Aug 2022 12:55:59: 2000000 INFO @ Tue, 02 Aug 2022 12:56:01: 7000000 INFO @ Tue, 02 Aug 2022 12:56:02: 12000000 INFO @ Tue, 02 Aug 2022 12:56:03: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:56:03: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:56:03: #1 total tags in treatment: 5615889 INFO @ Tue, 02 Aug 2022 12:56:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:56:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:56:03: #1 tags after filtering in treatment: 5425978 INFO @ Tue, 02 Aug 2022 12:56:03: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 12:56:03: #1 finished! INFO @ Tue, 02 Aug 2022 12:56:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:56:03: #2 number of paired peaks: 126 WARNING @ Tue, 02 Aug 2022 12:56:03: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 02 Aug 2022 12:56:03: start model_add_line... INFO @ Tue, 02 Aug 2022 12:56:03: start X-correlation... INFO @ Tue, 02 Aug 2022 12:56:03: end of X-cor INFO @ Tue, 02 Aug 2022 12:56:03: #2 finished! INFO @ Tue, 02 Aug 2022 12:56:03: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 12:56:03: #2 alternative fragment length(s) may be 77 bps INFO @ Tue, 02 Aug 2022 12:56:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.05_model.r WARNING @ Tue, 02 Aug 2022 12:56:03: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:56:03: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Tue, 02 Aug 2022 12:56:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:56:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:56:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:56:05: 3000000 INFO @ Tue, 02 Aug 2022 12:56:08: 8000000 INFO @ Tue, 02 Aug 2022 12:56:10: 4000000 INFO @ Tue, 02 Aug 2022 12:56:14: 9000000 INFO @ Tue, 02 Aug 2022 12:56:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:56:16: 5000000 INFO @ Tue, 02 Aug 2022 12:56:20: 10000000 INFO @ Tue, 02 Aug 2022 12:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:56:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.05_summits.bed INFO @ Tue, 02 Aug 2022 12:56:21: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (843 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:56:21: 6000000 INFO @ Tue, 02 Aug 2022 12:56:26: 11000000 INFO @ Tue, 02 Aug 2022 12:56:27: 7000000 INFO @ Tue, 02 Aug 2022 12:56:32: 12000000 INFO @ Tue, 02 Aug 2022 12:56:33: 8000000 INFO @ Tue, 02 Aug 2022 12:56:33: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:56:33: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:56:33: #1 total tags in treatment: 5615889 INFO @ Tue, 02 Aug 2022 12:56:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:56:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:56:33: #1 tags after filtering in treatment: 5425978 INFO @ Tue, 02 Aug 2022 12:56:33: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 12:56:33: #1 finished! INFO @ Tue, 02 Aug 2022 12:56:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:56:34: #2 number of paired peaks: 126 WARNING @ Tue, 02 Aug 2022 12:56:34: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 02 Aug 2022 12:56:34: start model_add_line... INFO @ Tue, 02 Aug 2022 12:56:34: start X-correlation... INFO @ Tue, 02 Aug 2022 12:56:34: end of X-cor INFO @ Tue, 02 Aug 2022 12:56:34: #2 finished! INFO @ Tue, 02 Aug 2022 12:56:34: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 12:56:34: #2 alternative fragment length(s) may be 77 bps INFO @ Tue, 02 Aug 2022 12:56:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.10_model.r WARNING @ Tue, 02 Aug 2022 12:56:34: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:56:34: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Tue, 02 Aug 2022 12:56:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:56:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:56:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:56:38: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:56:43: 10000000 INFO @ Tue, 02 Aug 2022 12:56:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:56:48: 11000000 INFO @ Tue, 02 Aug 2022 12:56:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:56:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:56:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.10_summits.bed INFO @ Tue, 02 Aug 2022 12:56:51: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (245 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:56:53: 12000000 INFO @ Tue, 02 Aug 2022 12:56:54: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:56:54: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:56:54: #1 total tags in treatment: 5615889 INFO @ Tue, 02 Aug 2022 12:56:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:56:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:56:54: #1 tags after filtering in treatment: 5425978 INFO @ Tue, 02 Aug 2022 12:56:54: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 12:56:54: #1 finished! INFO @ Tue, 02 Aug 2022 12:56:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:56:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:56:54: #2 number of paired peaks: 126 WARNING @ Tue, 02 Aug 2022 12:56:54: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 02 Aug 2022 12:56:54: start model_add_line... INFO @ Tue, 02 Aug 2022 12:56:54: start X-correlation... INFO @ Tue, 02 Aug 2022 12:56:54: end of X-cor INFO @ Tue, 02 Aug 2022 12:56:54: #2 finished! INFO @ Tue, 02 Aug 2022 12:56:54: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 12:56:54: #2 alternative fragment length(s) may be 77 bps INFO @ Tue, 02 Aug 2022 12:56:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.20_model.r WARNING @ Tue, 02 Aug 2022 12:56:54: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:56:54: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Tue, 02 Aug 2022 12:56:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:56:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:56:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:57:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:57:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:57:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:57:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX5847866/ERX5847866.20_summits.bed INFO @ Tue, 02 Aug 2022 12:57:12: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (98 records, 4 fields): 81 millis CompletedMACS2peakCalling