Job ID = 6626494 SRX = SRX5736473 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12085034 spots for SRR8956884/SRR8956884.sra Written 12085034 spots for SRR8956884/SRR8956884.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626718 ("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: 00:38:13 12085034 reads; of these: 12085034 (100.00%) were paired; of these: 1579997 (13.07%) aligned concordantly 0 times 6499637 (53.78%) aligned concordantly exactly 1 time 4005400 (33.14%) aligned concordantly >1 times ---- 1579997 pairs aligned concordantly 0 times; of these: 415843 (26.32%) aligned discordantly 1 time ---- 1164154 pairs aligned 0 times concordantly or discordantly; of these: 2328308 mates make up the pairs; of these: 1564699 (67.20%) aligned 0 times 294422 (12.65%) aligned exactly 1 time 469187 (20.15%) aligned >1 times 93.53% overall alignment rate Time searching: 00:38:13 Overall time: 00:38:13 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] 2337659 / 10874844 = 0.2150 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 07:53:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.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 07:53:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:53:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:53:06: 1000000 INFO @ Tue, 14 Jul 2020 07:53:12: 2000000 INFO @ Tue, 14 Jul 2020 07:53:19: 3000000 INFO @ Tue, 14 Jul 2020 07:53:25: 4000000 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 07:53:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.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 07:53:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:53:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:53:32: 5000000 INFO @ Tue, 14 Jul 2020 07:53:38: 1000000 INFO @ Tue, 14 Jul 2020 07:53:40: 6000000 INFO @ Tue, 14 Jul 2020 07:53:46: 2000000 INFO @ Tue, 14 Jul 2020 07:53:47: 7000000 INFO @ Tue, 14 Jul 2020 07:53:53: 3000000 INFO @ Tue, 14 Jul 2020 07:53:54: 8000000 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 07:54:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.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 07:54:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:54:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:54:01: 4000000 INFO @ Tue, 14 Jul 2020 07:54:02: 9000000 INFO @ Tue, 14 Jul 2020 07:54:07: 1000000 INFO @ Tue, 14 Jul 2020 07:54:09: 5000000 INFO @ Tue, 14 Jul 2020 07:54:09: 10000000 INFO @ Tue, 14 Jul 2020 07:54:15: 2000000 INFO @ Tue, 14 Jul 2020 07:54:17: 11000000 INFO @ Tue, 14 Jul 2020 07:54:17: 6000000 INFO @ Tue, 14 Jul 2020 07:54:23: 3000000 INFO @ Tue, 14 Jul 2020 07:54:24: 12000000 INFO @ Tue, 14 Jul 2020 07:54:24: 7000000 INFO @ Tue, 14 Jul 2020 07:54:30: 4000000 INFO @ Tue, 14 Jul 2020 07:54:32: 13000000 INFO @ Tue, 14 Jul 2020 07:54:32: 8000000 INFO @ Tue, 14 Jul 2020 07:54:38: 5000000 INFO @ Tue, 14 Jul 2020 07:54:39: 14000000 INFO @ Tue, 14 Jul 2020 07:54:40: 9000000 INFO @ Tue, 14 Jul 2020 07:54:46: 6000000 INFO @ Tue, 14 Jul 2020 07:54:47: 15000000 INFO @ Tue, 14 Jul 2020 07:54:48: 10000000 INFO @ Tue, 14 Jul 2020 07:54:53: 7000000 INFO @ Tue, 14 Jul 2020 07:54:54: 16000000 INFO @ Tue, 14 Jul 2020 07:54:56: 11000000 INFO @ Tue, 14 Jul 2020 07:55:01: 8000000 INFO @ Tue, 14 Jul 2020 07:55:02: 17000000 INFO @ Tue, 14 Jul 2020 07:55:04: 12000000 INFO @ Tue, 14 Jul 2020 07:55:08: 9000000 INFO @ Tue, 14 Jul 2020 07:55:09: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:55:09: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:55:09: #1 total tags in treatment: 8254177 INFO @ Tue, 14 Jul 2020 07:55:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:55:09: #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 07:55:09: #1 tags after filtering in treatment: 7512775 INFO @ Tue, 14 Jul 2020 07:55:09: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 07:55:09: #1 finished! INFO @ Tue, 14 Jul 2020 07:55:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:55:09: #2 number of paired peaks: 226 WARNING @ Tue, 14 Jul 2020 07:55:09: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 14 Jul 2020 07:55:09: start model_add_line... INFO @ Tue, 14 Jul 2020 07:55:09: start X-correlation... INFO @ Tue, 14 Jul 2020 07:55:09: end of X-cor INFO @ Tue, 14 Jul 2020 07:55:09: #2 finished! INFO @ Tue, 14 Jul 2020 07:55:09: #2 predicted fragment length is 125 bps INFO @ Tue, 14 Jul 2020 07:55:09: #2 alternative fragment length(s) may be 125 bps INFO @ Tue, 14 Jul 2020 07:55:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.05_model.r WARNING @ Tue, 14 Jul 2020 07:55:09: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:55:09: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Tue, 14 Jul 2020 07:55:09: #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 07:55:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:55:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:55:13: 13000000 INFO @ Tue, 14 Jul 2020 07:55:16: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:55:21: 14000000 INFO @ Tue, 14 Jul 2020 07:55:24: 11000000 INFO @ Tue, 14 Jul 2020 07:55:25: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:55:30: 15000000 INFO @ Tue, 14 Jul 2020 07:55:32: 12000000 INFO @ Tue, 14 Jul 2020 07:55:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:55:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:55:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.05_summits.bed INFO @ Tue, 14 Jul 2020 07:55:33: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3501 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:55:39: 16000000 INFO @ Tue, 14 Jul 2020 07:55:40: 13000000 INFO @ Tue, 14 Jul 2020 07:55:47: 14000000 INFO @ Tue, 14 Jul 2020 07:55:47: 17000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:55:55: 15000000 INFO @ Tue, 14 Jul 2020 07:55:55: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:55:55: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:55:55: #1 total tags in treatment: 8254177 INFO @ Tue, 14 Jul 2020 07:55:55: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:55:55: #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 07:55:55: #1 tags after filtering in treatment: 7512775 INFO @ Tue, 14 Jul 2020 07:55:55: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 07:55:55: #1 finished! INFO @ Tue, 14 Jul 2020 07:55:55: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:55:56: #2 number of paired peaks: 226 WARNING @ Tue, 14 Jul 2020 07:55:56: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 14 Jul 2020 07:55:56: start model_add_line... INFO @ Tue, 14 Jul 2020 07:55:56: start X-correlation... INFO @ Tue, 14 Jul 2020 07:55:56: end of X-cor INFO @ Tue, 14 Jul 2020 07:55:56: #2 finished! INFO @ Tue, 14 Jul 2020 07:55:56: #2 predicted fragment length is 125 bps INFO @ Tue, 14 Jul 2020 07:55:56: #2 alternative fragment length(s) may be 125 bps INFO @ Tue, 14 Jul 2020 07:55:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.10_model.r WARNING @ Tue, 14 Jul 2020 07:55:56: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:55:56: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Tue, 14 Jul 2020 07:55:56: #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 07:55:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:55:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:56:03: 16000000 INFO @ Tue, 14 Jul 2020 07:56:10: 17000000 INFO @ Tue, 14 Jul 2020 07:56:12: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:56:17: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:56:17: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:56:17: #1 total tags in treatment: 8254177 INFO @ Tue, 14 Jul 2020 07:56:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:56:17: #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 07:56:17: #1 tags after filtering in treatment: 7512775 INFO @ Tue, 14 Jul 2020 07:56:17: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 07:56:17: #1 finished! INFO @ Tue, 14 Jul 2020 07:56:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:56:17: #2 number of paired peaks: 226 WARNING @ Tue, 14 Jul 2020 07:56:17: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 14 Jul 2020 07:56:17: start model_add_line... INFO @ Tue, 14 Jul 2020 07:56:17: start X-correlation... INFO @ Tue, 14 Jul 2020 07:56:17: end of X-cor INFO @ Tue, 14 Jul 2020 07:56:17: #2 finished! INFO @ Tue, 14 Jul 2020 07:56:17: #2 predicted fragment length is 125 bps INFO @ Tue, 14 Jul 2020 07:56:17: #2 alternative fragment length(s) may be 125 bps INFO @ Tue, 14 Jul 2020 07:56:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.20_model.r WARNING @ Tue, 14 Jul 2020 07:56:17: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:56:17: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Tue, 14 Jul 2020 07:56:17: #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 07:56:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:56:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:56:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:56:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.10_summits.bed INFO @ Tue, 14 Jul 2020 07:56:21: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1105 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:56:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:56:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:56:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:56:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736473/SRX5736473.20_summits.bed INFO @ Tue, 14 Jul 2020 07:56:41: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 2 millis CompletedMACS2peakCalling