Job ID = 10714460 sra ファイルのダウンロード中... Completed: 1123666K bytes transferred in 22 seconds (412392K 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 17630602 spots for /home/okishinya/chipatlas/results/ce10/SRX4085376/SRR7167405.sra Written 17630602 spots for /home/okishinya/chipatlas/results/ce10/SRX4085376/SRR7167405.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: 00:13:24 17630602 reads; of these: 17630602 (100.00%) were paired; of these: 9436717 (53.52%) aligned concordantly 0 times 6977686 (39.58%) aligned concordantly exactly 1 time 1216199 (6.90%) aligned concordantly >1 times ---- 9436717 pairs aligned concordantly 0 times; of these: 475108 (5.03%) aligned discordantly 1 time ---- 8961609 pairs aligned 0 times concordantly or discordantly; of these: 17923218 mates make up the pairs; of these: 13000251 (72.53%) aligned 0 times 4329557 (24.16%) aligned exactly 1 time 593410 (3.31%) aligned >1 times 63.13% overall alignment rate Time searching: 00:13:24 Overall time: 00:13:24 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] 553740 / 8512669 = 0.0650 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, 03 Jun 2018 13:01:00: # Command line: callpeak -t SRX4085376.bam -f BAM -g ce -n SRX4085376.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085376.10 # format = BAM # ChIP-seq file = ['SRX4085376.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 @ Sun, 03 Jun 2018 13:01:00: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:01:00: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:01:00: # Command line: callpeak -t SRX4085376.bam -f BAM -g ce -n SRX4085376.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085376.05 # format = BAM # ChIP-seq file = ['SRX4085376.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 @ Sun, 03 Jun 2018 13:01:00: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:01:00: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:01:00: # Command line: callpeak -t SRX4085376.bam -f BAM -g ce -n SRX4085376.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085376.20 # format = BAM # ChIP-seq file = ['SRX4085376.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 @ Sun, 03 Jun 2018 13:01:00: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:01:00: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:01:06: 1000000 INFO @ Sun, 03 Jun 2018 13:01:06: 1000000 INFO @ Sun, 03 Jun 2018 13:01:06: 1000000 INFO @ Sun, 03 Jun 2018 13:01:12: 2000000 INFO @ Sun, 03 Jun 2018 13:01:12: 2000000 INFO @ Sun, 03 Jun 2018 13:01:13: 2000000 INFO @ Sun, 03 Jun 2018 13:01:18: 3000000 INFO @ Sun, 03 Jun 2018 13:01:18: 3000000 INFO @ Sun, 03 Jun 2018 13:01:19: 3000000 INFO @ Sun, 03 Jun 2018 13:01:24: 4000000 INFO @ Sun, 03 Jun 2018 13:01:24: 4000000 INFO @ Sun, 03 Jun 2018 13:01:25: 4000000 INFO @ Sun, 03 Jun 2018 13:01:30: 5000000 INFO @ Sun, 03 Jun 2018 13:01:30: 5000000 INFO @ Sun, 03 Jun 2018 13:01:30: 5000000 INFO @ Sun, 03 Jun 2018 13:01:37: 6000000 INFO @ Sun, 03 Jun 2018 13:01:37: 6000000 INFO @ Sun, 03 Jun 2018 13:01:37: 6000000 INFO @ Sun, 03 Jun 2018 13:01:44: 7000000 INFO @ Sun, 03 Jun 2018 13:01:44: 7000000 INFO @ Sun, 03 Jun 2018 13:01:45: 7000000 INFO @ Sun, 03 Jun 2018 13:01:51: 8000000 INFO @ Sun, 03 Jun 2018 13:01:51: 8000000 INFO @ Sun, 03 Jun 2018 13:01:52: 8000000 INFO @ Sun, 03 Jun 2018 13:01:58: 9000000 INFO @ Sun, 03 Jun 2018 13:01:58: 9000000 INFO @ Sun, 03 Jun 2018 13:02:00: 9000000 INFO @ Sun, 03 Jun 2018 13:02:04: 10000000 INFO @ Sun, 03 Jun 2018 13:02:04: 10000000 INFO @ Sun, 03 Jun 2018 13:02:07: 10000000 INFO @ Sun, 03 Jun 2018 13:02:11: 11000000 INFO @ Sun, 03 Jun 2018 13:02:11: 11000000 INFO @ Sun, 03 Jun 2018 13:02:15: 11000000 INFO @ Sun, 03 Jun 2018 13:02:18: 12000000 INFO @ Sun, 03 Jun 2018 13:02:18: 12000000 INFO @ Sun, 03 Jun 2018 13:02:22: 12000000 INFO @ Sun, 03 Jun 2018 13:02:25: 13000000 INFO @ Sun, 03 Jun 2018 13:02:25: 13000000 INFO @ Sun, 03 Jun 2018 13:02:30: 13000000 INFO @ Sun, 03 Jun 2018 13:02:32: 14000000 INFO @ Sun, 03 Jun 2018 13:02:32: 14000000 INFO @ Sun, 03 Jun 2018 13:02:37: 14000000 INFO @ Sun, 03 Jun 2018 13:02:39: 15000000 INFO @ Sun, 03 Jun 2018 13:02:39: 15000000 INFO @ Sun, 03 Jun 2018 13:02:44: 15000000 INFO @ Sun, 03 Jun 2018 13:02:46: 16000000 INFO @ Sun, 03 Jun 2018 13:02:46: 16000000 INFO @ Sun, 03 Jun 2018 13:02:52: 16000000 INFO @ Sun, 03 Jun 2018 13:02:53: 17000000 INFO @ Sun, 03 Jun 2018 13:02:53: 17000000 INFO @ Sun, 03 Jun 2018 13:02:59: 17000000 INFO @ Sun, 03 Jun 2018 13:03:00: 18000000 INFO @ Sun, 03 Jun 2018 13:03:00: 18000000 INFO @ Sun, 03 Jun 2018 13:03:06: 19000000 INFO @ Sun, 03 Jun 2018 13:03:06: 19000000 INFO @ Sun, 03 Jun 2018 13:03:07: 18000000 INFO @ Sun, 03 Jun 2018 13:03:13: 20000000 INFO @ Sun, 03 Jun 2018 13:03:13: 20000000 INFO @ Sun, 03 Jun 2018 13:03:14: 19000000 INFO @ Sun, 03 Jun 2018 13:03:19: 21000000 INFO @ Sun, 03 Jun 2018 13:03:19: 21000000 INFO @ Sun, 03 Jun 2018 13:03:20: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:03:20: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:03:20: #1 total tags in treatment: 7661004 INFO @ Sun, 03 Jun 2018 13:03:20: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:03:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:03:20: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:03:20: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:03:20: #1 total tags in treatment: 7661004 INFO @ Sun, 03 Jun 2018 13:03:20: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:03:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:03:20: #1 tags after filtering in treatment: 6725991 INFO @ Sun, 03 Jun 2018 13:03:20: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 13:03:20: #1 finished! INFO @ Sun, 03 Jun 2018 13:03:20: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:03:20: #1 tags after filtering in treatment: 6725991 INFO @ Sun, 03 Jun 2018 13:03:20: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 13:03:20: #1 finished! INFO @ Sun, 03 Jun 2018 13:03:20: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:03:21: #2 number of paired peaks: 513 WARNING @ Sun, 03 Jun 2018 13:03:21: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Sun, 03 Jun 2018 13:03:21: start model_add_line... INFO @ Sun, 03 Jun 2018 13:03:21: #2 number of paired peaks: 513 WARNING @ Sun, 03 Jun 2018 13:03:21: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Sun, 03 Jun 2018 13:03:21: start model_add_line... INFO @ Sun, 03 Jun 2018 13:03:21: start X-correlation... INFO @ Sun, 03 Jun 2018 13:03:21: end of X-cor INFO @ Sun, 03 Jun 2018 13:03:21: #2 finished! INFO @ Sun, 03 Jun 2018 13:03:21: #2 predicted fragment length is 90 bps INFO @ Sun, 03 Jun 2018 13:03:21: #2 alternative fragment length(s) may be 90 bps INFO @ Sun, 03 Jun 2018 13:03:21: #2.2 Generate R script for model : SRX4085376.05_model.r INFO @ Sun, 03 Jun 2018 13:03:21: start X-correlation... WARNING @ Sun, 03 Jun 2018 13:03:21: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:03:21: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sun, 03 Jun 2018 13:03:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:03:21: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:03:21: end of X-cor INFO @ Sun, 03 Jun 2018 13:03:21: #2 finished! INFO @ Sun, 03 Jun 2018 13:03:21: #2 predicted fragment length is 90 bps INFO @ Sun, 03 Jun 2018 13:03:21: #2 alternative fragment length(s) may be 90 bps INFO @ Sun, 03 Jun 2018 13:03:21: #2.2 Generate R script for model : SRX4085376.10_model.r INFO @ Sun, 03 Jun 2018 13:03:21: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 03 Jun 2018 13:03:21: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:03:21: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sun, 03 Jun 2018 13:03:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:03:21: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:03:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:03:22: 20000000 INFO @ Sun, 03 Jun 2018 13:03:28: 21000000 INFO @ Sun, 03 Jun 2018 13:03:29: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:03:29: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:03:29: #1 total tags in treatment: 7661004 INFO @ Sun, 03 Jun 2018 13:03:29: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:03:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:03:29: #1 tags after filtering in treatment: 6725991 INFO @ Sun, 03 Jun 2018 13:03:29: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 03 Jun 2018 13:03:29: #1 finished! INFO @ Sun, 03 Jun 2018 13:03:29: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:03:30: #2 number of paired peaks: 513 WARNING @ Sun, 03 Jun 2018 13:03:30: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Sun, 03 Jun 2018 13:03:30: start model_add_line... INFO @ Sun, 03 Jun 2018 13:03:30: start X-correlation... INFO @ Sun, 03 Jun 2018 13:03:30: end of X-cor INFO @ Sun, 03 Jun 2018 13:03:30: #2 finished! INFO @ Sun, 03 Jun 2018 13:03:30: #2 predicted fragment length is 90 bps INFO @ Sun, 03 Jun 2018 13:03:30: #2 alternative fragment length(s) may be 90 bps INFO @ Sun, 03 Jun 2018 13:03:30: #2.2 Generate R script for model : SRX4085376.20_model.r WARNING @ Sun, 03 Jun 2018 13:03:30: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:03:30: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sun, 03 Jun 2018 13:03:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:03:30: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:03:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:03:37: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:03:38: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:03:45: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:03:46: #4 Write output xls file... SRX4085376.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:03:46: #4 Write peak in narrowPeak format file... SRX4085376.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:03:46: #4 Write summits bed file... SRX4085376.05_summits.bed INFO @ Sun, 03 Jun 2018 13:03:46: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3338 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:03:47: #4 Write output xls file... SRX4085376.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:03:47: #4 Write peak in narrowPeak format file... SRX4085376.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:03:47: #4 Write summits bed file... SRX4085376.10_summits.bed INFO @ Sun, 03 Jun 2018 13:03:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1954 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:03:54: #4 Write output xls file... SRX4085376.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:03:54: #4 Write peak in narrowPeak format file... SRX4085376.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:03:54: #4 Write summits bed file... SRX4085376.20_summits.bed INFO @ Sun, 03 Jun 2018 13:03:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (901 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。