Job ID = 11597693 sra ファイルのダウンロード中... Completed: 3111310K bytes transferred in 39 seconds (646890K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 27454854 spots for /home/okishinya/chipatlas/results/ce10/SRX5064641/SRR8246577.sra Written 27454854 spots for /home/okishinya/chipatlas/results/ce10/SRX5064641/SRR8246577.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:22:14 27454854 reads; of these: 27454854 (100.00%) were paired; of these: 21388732 (77.91%) aligned concordantly 0 times 5382180 (19.60%) aligned concordantly exactly 1 time 683942 (2.49%) aligned concordantly >1 times ---- 21388732 pairs aligned concordantly 0 times; of these: 59259 (0.28%) aligned discordantly 1 time ---- 21329473 pairs aligned 0 times concordantly or discordantly; of these: 42658946 mates make up the pairs; of these: 42334757 (99.24%) aligned 0 times 261032 (0.61%) aligned exactly 1 time 63157 (0.15%) aligned >1 times 22.90% overall alignment rate Time searching: 00:22:14 Overall time: 00:22:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 2725884 / 6116462 = 0.4457 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Wed, 30 Jan 2019 14:50:43: # Command line: callpeak -t SRX5064641.bam -f BAM -g ce -n SRX5064641.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5064641.10 # format = BAM # ChIP-seq file = ['SRX5064641.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 30 Jan 2019 14:50:43: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:50:43: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:50:43: # Command line: callpeak -t SRX5064641.bam -f BAM -g ce -n SRX5064641.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5064641.20 # format = BAM # ChIP-seq file = ['SRX5064641.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 30 Jan 2019 14:50:43: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:50:43: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:50:43: # Command line: callpeak -t SRX5064641.bam -f BAM -g ce -n SRX5064641.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5064641.05 # format = BAM # ChIP-seq file = ['SRX5064641.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 30 Jan 2019 14:50:43: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:50:43: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:50:53: 1000000 INFO @ Wed, 30 Jan 2019 14:50:53: 1000000 INFO @ Wed, 30 Jan 2019 14:50:53: 1000000 INFO @ Wed, 30 Jan 2019 14:51:03: 2000000 INFO @ Wed, 30 Jan 2019 14:51:03: 2000000 INFO @ Wed, 30 Jan 2019 14:51:03: 2000000 INFO @ Wed, 30 Jan 2019 14:51:13: 3000000 INFO @ Wed, 30 Jan 2019 14:51:13: 3000000 INFO @ Wed, 30 Jan 2019 14:51:13: 3000000 INFO @ Wed, 30 Jan 2019 14:51:23: 4000000 INFO @ Wed, 30 Jan 2019 14:51:23: 4000000 INFO @ Wed, 30 Jan 2019 14:51:24: 4000000 INFO @ Wed, 30 Jan 2019 14:51:32: 5000000 INFO @ Wed, 30 Jan 2019 14:51:32: 5000000 INFO @ Wed, 30 Jan 2019 14:51:32: 5000000 INFO @ Wed, 30 Jan 2019 14:51:41: 6000000 INFO @ Wed, 30 Jan 2019 14:51:43: 6000000 INFO @ Wed, 30 Jan 2019 14:51:43: 6000000 INFO @ Wed, 30 Jan 2019 14:51:52: 7000000 INFO @ Wed, 30 Jan 2019 14:51:52: 7000000 INFO @ Wed, 30 Jan 2019 14:51:52: 7000000 INFO @ Wed, 30 Jan 2019 14:51:53: #1 tag size is determined as 150 bps INFO @ Wed, 30 Jan 2019 14:51:53: #1 tag size = 150 INFO @ Wed, 30 Jan 2019 14:51:53: #1 total tags in treatment: 3354868 INFO @ Wed, 30 Jan 2019 14:51:53: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:51:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:51:53: #1 tag size is determined as 150 bps INFO @ Wed, 30 Jan 2019 14:51:53: #1 tag size = 150 INFO @ Wed, 30 Jan 2019 14:51:53: #1 total tags in treatment: 3354868 INFO @ Wed, 30 Jan 2019 14:51:53: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:51:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:51:53: #1 tags after filtering in treatment: 3222885 INFO @ Wed, 30 Jan 2019 14:51:53: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 30 Jan 2019 14:51:53: #1 finished! INFO @ Wed, 30 Jan 2019 14:51:53: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:51:53: #1 tags after filtering in treatment: 3222885 INFO @ Wed, 30 Jan 2019 14:51:53: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 30 Jan 2019 14:51:53: #1 finished! INFO @ Wed, 30 Jan 2019 14:51:53: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:51:53: #1 tag size is determined as 150 bps INFO @ Wed, 30 Jan 2019 14:51:53: #1 tag size = 150 INFO @ Wed, 30 Jan 2019 14:51:53: #1 total tags in treatment: 3354868 INFO @ Wed, 30 Jan 2019 14:51:53: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:51:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:51:53: #2 number of paired peaks: 325 WARNING @ Wed, 30 Jan 2019 14:51:53: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Wed, 30 Jan 2019 14:51:53: start model_add_line... INFO @ Wed, 30 Jan 2019 14:51:54: start X-correlation... INFO @ Wed, 30 Jan 2019 14:51:54: #1 tags after filtering in treatment: 3222885 INFO @ Wed, 30 Jan 2019 14:51:54: #1 Redundant rate of treatment: 0.04 INFO @ Wed, 30 Jan 2019 14:51:54: #1 finished! INFO @ Wed, 30 Jan 2019 14:51:54: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:51:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:51:54: end of X-cor INFO @ Wed, 30 Jan 2019 14:51:54: #2 finished! INFO @ Wed, 30 Jan 2019 14:51:54: #2 predicted fragment length is 222 bps INFO @ Wed, 30 Jan 2019 14:51:54: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 30 Jan 2019 14:51:54: #2.2 Generate R script for model : SRX5064641.10_model.r WARNING @ Wed, 30 Jan 2019 14:51:54: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:51:54: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Wed, 30 Jan 2019 14:51:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:51:54: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:51:54: #2 number of paired peaks: 325 WARNING @ Wed, 30 Jan 2019 14:51:54: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Wed, 30 Jan 2019 14:51:54: start model_add_line... INFO @ Wed, 30 Jan 2019 14:51:54: start X-correlation... INFO @ Wed, 30 Jan 2019 14:51:54: end of X-cor INFO @ Wed, 30 Jan 2019 14:51:54: #2 finished! INFO @ Wed, 30 Jan 2019 14:51:54: #2 predicted fragment length is 222 bps INFO @ Wed, 30 Jan 2019 14:51:54: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 30 Jan 2019 14:51:54: #2.2 Generate R script for model : SRX5064641.20_model.r WARNING @ Wed, 30 Jan 2019 14:51:54: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:51:54: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Wed, 30 Jan 2019 14:51:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:51:54: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:51:54: #2 number of paired peaks: 325 WARNING @ Wed, 30 Jan 2019 14:51:54: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Wed, 30 Jan 2019 14:51:54: start model_add_line... INFO @ Wed, 30 Jan 2019 14:51:54: start X-correlation... INFO @ Wed, 30 Jan 2019 14:51:54: end of X-cor INFO @ Wed, 30 Jan 2019 14:51:54: #2 finished! INFO @ Wed, 30 Jan 2019 14:51:54: #2 predicted fragment length is 222 bps INFO @ Wed, 30 Jan 2019 14:51:54: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 30 Jan 2019 14:51:54: #2.2 Generate R script for model : SRX5064641.05_model.r WARNING @ Wed, 30 Jan 2019 14:51:54: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:51:54: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Wed, 30 Jan 2019 14:51:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:51:54: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:52:02: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:52:02: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:52:02: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:52:06: #4 Write output xls file... SRX5064641.10_peaks.xls INFO @ Wed, 30 Jan 2019 14:52:06: #4 Write peak in narrowPeak format file... SRX5064641.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:52:06: #4 Write summits bed file... SRX5064641.10_summits.bed INFO @ Wed, 30 Jan 2019 14:52:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (198 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 14:52:06: #4 Write output xls file... SRX5064641.20_peaks.xls INFO @ Wed, 30 Jan 2019 14:52:06: #4 Write peak in narrowPeak format file... SRX5064641.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:52:06: #4 Write summits bed file... SRX5064641.20_summits.bed INFO @ Wed, 30 Jan 2019 14:52:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (123 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 14:52:06: #4 Write output xls file... SRX5064641.05_peaks.xls INFO @ Wed, 30 Jan 2019 14:52:06: #4 Write peak in narrowPeak format file... SRX5064641.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:52:06: #4 Write summits bed file... SRX5064641.05_summits.bed INFO @ Wed, 30 Jan 2019 14:52:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (277 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。