Job ID = 6626573 SRX = SRX7224575 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7770850 spots for SRR10541129/SRR10541129.sra Written 7770850 spots for SRR10541129/SRR10541129.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626741 ("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: 00:24:47 7770850 reads; of these: 7770850 (100.00%) were paired; of these: 2298757 (29.58%) aligned concordantly 0 times 4327144 (55.68%) aligned concordantly exactly 1 time 1144949 (14.73%) aligned concordantly >1 times ---- 2298757 pairs aligned concordantly 0 times; of these: 1313230 (57.13%) aligned discordantly 1 time ---- 985527 pairs aligned 0 times concordantly or discordantly; of these: 1971054 mates make up the pairs; of these: 1185195 (60.13%) aligned 0 times 186967 (9.49%) aligned exactly 1 time 598892 (30.38%) aligned >1 times 92.37% overall alignment rate Time searching: 00:24:47 Overall time: 00:24:47 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 12 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] 857856 / 6668863 = 0.1286 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:06:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.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, 14 Jul 2020 08:06:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:06:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:07:05: 1000000 INFO @ Tue, 14 Jul 2020 08:07:16: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:07:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.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, 14 Jul 2020 08:07:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:07:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:07:26: 3000000 INFO @ Tue, 14 Jul 2020 08:07:36: 1000000 INFO @ Tue, 14 Jul 2020 08:07:37: 4000000 INFO @ Tue, 14 Jul 2020 08:07:48: 2000000 INFO @ Tue, 14 Jul 2020 08:07:48: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:07:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.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, 14 Jul 2020 08:07:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:07:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:07:59: 6000000 INFO @ Tue, 14 Jul 2020 08:07:59: 3000000 INFO @ Tue, 14 Jul 2020 08:08:06: 1000000 INFO @ Tue, 14 Jul 2020 08:08:11: 4000000 INFO @ Tue, 14 Jul 2020 08:08:11: 7000000 INFO @ Tue, 14 Jul 2020 08:08:18: 2000000 INFO @ Tue, 14 Jul 2020 08:08:23: 5000000 INFO @ Tue, 14 Jul 2020 08:08:23: 8000000 INFO @ Tue, 14 Jul 2020 08:08:29: 3000000 INFO @ Tue, 14 Jul 2020 08:08:35: 6000000 INFO @ Tue, 14 Jul 2020 08:08:35: 9000000 INFO @ Tue, 14 Jul 2020 08:08:41: 4000000 INFO @ Tue, 14 Jul 2020 08:08:46: 7000000 INFO @ Tue, 14 Jul 2020 08:08:48: 10000000 INFO @ Tue, 14 Jul 2020 08:08:53: 5000000 INFO @ Tue, 14 Jul 2020 08:08:56: 8000000 INFO @ Tue, 14 Jul 2020 08:09:00: 11000000 INFO @ Tue, 14 Jul 2020 08:09:05: 6000000 INFO @ Tue, 14 Jul 2020 08:09:07: 9000000 INFO @ Tue, 14 Jul 2020 08:09:12: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:09:16: 7000000 INFO @ Tue, 14 Jul 2020 08:09:18: 10000000 INFO @ Tue, 14 Jul 2020 08:09:19: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 08:09:19: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 08:09:19: #1 total tags in treatment: 4747765 INFO @ Tue, 14 Jul 2020 08:09:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:09:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:09:19: #1 tags after filtering in treatment: 4571823 INFO @ Tue, 14 Jul 2020 08:09:19: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 08:09:19: #1 finished! INFO @ Tue, 14 Jul 2020 08:09:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:09:20: #2 number of paired peaks: 303 WARNING @ Tue, 14 Jul 2020 08:09:20: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Tue, 14 Jul 2020 08:09:20: start model_add_line... INFO @ Tue, 14 Jul 2020 08:09:20: start X-correlation... INFO @ Tue, 14 Jul 2020 08:09:20: end of X-cor INFO @ Tue, 14 Jul 2020 08:09:20: #2 finished! INFO @ Tue, 14 Jul 2020 08:09:20: #2 predicted fragment length is 187 bps INFO @ Tue, 14 Jul 2020 08:09:20: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 14 Jul 2020 08:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.05_model.r WARNING @ Tue, 14 Jul 2020 08:09:20: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:09:20: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Tue, 14 Jul 2020 08:09:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:09:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:09:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:09:26: 8000000 INFO @ Tue, 14 Jul 2020 08:09:29: 11000000 INFO @ Tue, 14 Jul 2020 08:09:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:09:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:09:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:09:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.05_summits.bed INFO @ Tue, 14 Jul 2020 08:09:36: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (836 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:09:38: 9000000 INFO @ Tue, 14 Jul 2020 08:09:40: 12000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:09:47: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 08:09:47: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 08:09:47: #1 total tags in treatment: 4747765 INFO @ Tue, 14 Jul 2020 08:09:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:09:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:09:47: #1 tags after filtering in treatment: 4571823 INFO @ Tue, 14 Jul 2020 08:09:47: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 08:09:47: #1 finished! INFO @ Tue, 14 Jul 2020 08:09:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:09:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:09:47: #2 number of paired peaks: 303 WARNING @ Tue, 14 Jul 2020 08:09:47: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Tue, 14 Jul 2020 08:09:47: start model_add_line... INFO @ Tue, 14 Jul 2020 08:09:47: start X-correlation... INFO @ Tue, 14 Jul 2020 08:09:47: end of X-cor INFO @ Tue, 14 Jul 2020 08:09:47: #2 finished! INFO @ Tue, 14 Jul 2020 08:09:47: #2 predicted fragment length is 187 bps INFO @ Tue, 14 Jul 2020 08:09:47: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 14 Jul 2020 08:09:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.10_model.r WARNING @ Tue, 14 Jul 2020 08:09:47: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:09:47: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Tue, 14 Jul 2020 08:09:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:09:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:09:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:09:49: 10000000 INFO @ Tue, 14 Jul 2020 08:09:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:09:59: 11000000 INFO @ Tue, 14 Jul 2020 08:10:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:10:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:10:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.10_summits.bed INFO @ Tue, 14 Jul 2020 08:10:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (506 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:10:09: 12000000 INFO @ Tue, 14 Jul 2020 08:10:15: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 08:10:15: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 08:10:15: #1 total tags in treatment: 4747765 INFO @ Tue, 14 Jul 2020 08:10:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:10:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:10:16: #1 tags after filtering in treatment: 4571823 INFO @ Tue, 14 Jul 2020 08:10:16: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 08:10:16: #1 finished! INFO @ Tue, 14 Jul 2020 08:10:16: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:10:16: #2 number of paired peaks: 303 WARNING @ Tue, 14 Jul 2020 08:10:16: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Tue, 14 Jul 2020 08:10:16: start model_add_line... INFO @ Tue, 14 Jul 2020 08:10:16: start X-correlation... INFO @ Tue, 14 Jul 2020 08:10:16: end of X-cor INFO @ Tue, 14 Jul 2020 08:10:16: #2 finished! INFO @ Tue, 14 Jul 2020 08:10:16: #2 predicted fragment length is 187 bps INFO @ Tue, 14 Jul 2020 08:10:16: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 14 Jul 2020 08:10:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.20_model.r WARNING @ Tue, 14 Jul 2020 08:10:16: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:10:16: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Tue, 14 Jul 2020 08:10:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:10:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:10:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:10:26: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:10:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:10:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:10:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224575/SRX7224575.20_summits.bed INFO @ Tue, 14 Jul 2020 08:10:31: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (264 records, 4 fields): 62 millis CompletedMACS2peakCalling