Job ID = 11293716 sra ファイルのダウンロード中... Completed: 255418K bytes transferred in 10 seconds (202427K 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 3109819 spots for /home/okishinya/chipatlas/results/dm3/SRX4940247/SRR8113880.sra Written 3109819 spots for /home/okishinya/chipatlas/results/dm3/SRX4940247/SRR8113880.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: 00:06:49 3109819 reads; of these: 3109819 (100.00%) were paired; of these: 353363 (11.36%) aligned concordantly 0 times 2292508 (73.72%) aligned concordantly exactly 1 time 463948 (14.92%) aligned concordantly >1 times ---- 353363 pairs aligned concordantly 0 times; of these: 101125 (28.62%) aligned discordantly 1 time ---- 252238 pairs aligned 0 times concordantly or discordantly; of these: 504476 mates make up the pairs; of these: 366011 (72.55%) aligned 0 times 81247 (16.11%) aligned exactly 1 time 57218 (11.34%) aligned >1 times 94.12% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 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_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] 63388 / 2849443 = 0.0222 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 @ Sun, 04 Nov 2018 17:57:33: # Command line: callpeak -t SRX4940247.bam -f BAM -g dm -n SRX4940247.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4940247.10 # format = BAM # ChIP-seq file = ['SRX4940247.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 @ Sun, 04 Nov 2018 17:57:33: # Command line: callpeak -t SRX4940247.bam -f BAM -g dm -n SRX4940247.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4940247.20 # format = BAM # ChIP-seq file = ['SRX4940247.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 @ Sun, 04 Nov 2018 17:57:33: # Command line: callpeak -t SRX4940247.bam -f BAM -g dm -n SRX4940247.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4940247.05 # format = BAM # ChIP-seq file = ['SRX4940247.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 @ Sun, 04 Nov 2018 17:57:33: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:57:33: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:57:33: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:57:33: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:33: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:33: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:57:41: 1000000 INFO @ Sun, 04 Nov 2018 17:57:41: 1000000 INFO @ Sun, 04 Nov 2018 17:57:41: 1000000 INFO @ Sun, 04 Nov 2018 17:57:48: 2000000 INFO @ Sun, 04 Nov 2018 17:57:49: 2000000 INFO @ Sun, 04 Nov 2018 17:57:49: 2000000 INFO @ Sun, 04 Nov 2018 17:57:56: 3000000 INFO @ Sun, 04 Nov 2018 17:57:56: 3000000 INFO @ Sun, 04 Nov 2018 17:57:56: 3000000 INFO @ Sun, 04 Nov 2018 17:58:03: 4000000 INFO @ Sun, 04 Nov 2018 17:58:04: 4000000 INFO @ Sun, 04 Nov 2018 17:58:04: 4000000 INFO @ Sun, 04 Nov 2018 17:58:11: 5000000 INFO @ Sun, 04 Nov 2018 17:58:12: 5000000 INFO @ Sun, 04 Nov 2018 17:58:12: 5000000 INFO @ Sun, 04 Nov 2018 17:58:16: #1 tag size is determined as 75 bps INFO @ Sun, 04 Nov 2018 17:58:16: #1 tag size = 75 INFO @ Sun, 04 Nov 2018 17:58:16: #1 total tags in treatment: 2693650 INFO @ Sun, 04 Nov 2018 17:58:16: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:58:16: #1 tags after filtering in treatment: 2607104 INFO @ Sun, 04 Nov 2018 17:58:16: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 04 Nov 2018 17:58:16: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:16: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:16: #2 number of paired peaks: 138 WARNING @ Sun, 04 Nov 2018 17:58:16: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sun, 04 Nov 2018 17:58:16: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:17: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:17: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:17: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:17: #2 predicted fragment length is 101 bps INFO @ Sun, 04 Nov 2018 17:58:17: #2 alternative fragment length(s) may be 101 bps INFO @ Sun, 04 Nov 2018 17:58:17: #2.2 Generate R script for model : SRX4940247.05_model.r WARNING @ Sun, 04 Nov 2018 17:58:17: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:58:17: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sun, 04 Nov 2018 17:58:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:58:17: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:18: #1 tag size is determined as 75 bps INFO @ Sun, 04 Nov 2018 17:58:18: #1 tag size = 75 INFO @ Sun, 04 Nov 2018 17:58:18: #1 total tags in treatment: 2693650 INFO @ Sun, 04 Nov 2018 17:58:18: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:58:18: #1 tag size is determined as 75 bps INFO @ Sun, 04 Nov 2018 17:58:18: #1 tag size = 75 INFO @ Sun, 04 Nov 2018 17:58:18: #1 total tags in treatment: 2693650 INFO @ Sun, 04 Nov 2018 17:58:18: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:58:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:58:18: #1 tags after filtering in treatment: 2607104 INFO @ Sun, 04 Nov 2018 17:58:18: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 04 Nov 2018 17:58:18: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:18: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:18: #1 tags after filtering in treatment: 2607104 INFO @ Sun, 04 Nov 2018 17:58:18: #1 Redundant rate of treatment: 0.03 INFO @ Sun, 04 Nov 2018 17:58:18: #1 finished! INFO @ Sun, 04 Nov 2018 17:58:18: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:58:18: #2 number of paired peaks: 138 WARNING @ Sun, 04 Nov 2018 17:58:18: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sun, 04 Nov 2018 17:58:18: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:18: #2 number of paired peaks: 138 WARNING @ Sun, 04 Nov 2018 17:58:18: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sun, 04 Nov 2018 17:58:18: start model_add_line... INFO @ Sun, 04 Nov 2018 17:58:18: start X-correlation... INFO @ Sun, 04 Nov 2018 17:58:18: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:18: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:18: #2 predicted fragment length is 101 bps INFO @ Sun, 04 Nov 2018 17:58:18: #2 alternative fragment length(s) may be 101 bps INFO @ Sun, 04 Nov 2018 17:58:18: #2.2 Generate R script for model : SRX4940247.20_model.r INFO @ Sun, 04 Nov 2018 17:58:18: start X-correlation... WARNING @ Sun, 04 Nov 2018 17:58:18: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:58:18: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sun, 04 Nov 2018 17:58:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:58:18: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:18: end of X-cor INFO @ Sun, 04 Nov 2018 17:58:18: #2 finished! INFO @ Sun, 04 Nov 2018 17:58:18: #2 predicted fragment length is 101 bps INFO @ Sun, 04 Nov 2018 17:58:18: #2 alternative fragment length(s) may be 101 bps INFO @ Sun, 04 Nov 2018 17:58:18: #2.2 Generate R script for model : SRX4940247.10_model.r WARNING @ Sun, 04 Nov 2018 17:58:18: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:58:18: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sun, 04 Nov 2018 17:58:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:58:18: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:58:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:58:23: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:58:24: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:58:24: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:58:27: #4 Write output xls file... SRX4940247.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:58:27: #4 Write peak in narrowPeak format file... SRX4940247.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:58:27: #4 Write summits bed file... SRX4940247.05_summits.bed INFO @ Sun, 04 Nov 2018 17:58:27: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (123 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:58:28: #4 Write output xls file... SRX4940247.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:58:28: #4 Write peak in narrowPeak format file... SRX4940247.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:58:28: #4 Write summits bed file... SRX4940247.20_summits.bed INFO @ Sun, 04 Nov 2018 17:58:28: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (43 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:58:28: #4 Write output xls file... SRX4940247.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:58:28: #4 Write peak in narrowPeak format file... SRX4940247.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:58:28: #4 Write summits bed file... SRX4940247.10_summits.bed INFO @ Sun, 04 Nov 2018 17:58:28: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (60 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。