Job ID = 9162302 sra ファイルのダウンロード中... Completed: 545873K bytes transferred in 11 seconds (392629K bits/sec), in 1 file, 2 directories. 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... Written 4494555 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1872741/SRR3713214.sra Written 4494555 spots total 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: 00:05:32 4494555 reads; of these: 4494555 (100.00%) were paired; of these: 1119154 (24.90%) aligned concordantly 0 times 2892956 (64.37%) aligned concordantly exactly 1 time 482445 (10.73%) aligned concordantly >1 times ---- 1119154 pairs aligned concordantly 0 times; of these: 279934 (25.01%) aligned discordantly 1 time ---- 839220 pairs aligned 0 times concordantly or discordantly; of these: 1678440 mates make up the pairs; of these: 1511444 (90.05%) aligned 0 times 54645 (3.26%) aligned exactly 1 time 112351 (6.69%) aligned >1 times 83.19% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 93216 / 3634480 = 0.0256 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, 28 Jun 2017 07:23:56: # Command line: callpeak -t SRX1872741.bam -f BAM -g 12100000 -n SRX1872741.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872741.05 # format = BAM # ChIP-seq file = ['SRX1872741.bam'] # control file = None # effective genome size = 1.21e+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, 28 Jun 2017 07:23:56: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:23:56: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:23:56: # Command line: callpeak -t SRX1872741.bam -f BAM -g 12100000 -n SRX1872741.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872741.20 # format = BAM # ChIP-seq file = ['SRX1872741.bam'] # control file = None # effective genome size = 1.21e+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, 28 Jun 2017 07:23:56: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:23:56: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:23:56: # Command line: callpeak -t SRX1872741.bam -f BAM -g 12100000 -n SRX1872741.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872741.10 # format = BAM # ChIP-seq file = ['SRX1872741.bam'] # control file = None # effective genome size = 1.21e+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, 28 Jun 2017 07:23:56: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:23:56: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:24:05: 1000000 INFO @ Wed, 28 Jun 2017 07:24:07: 1000000 INFO @ Wed, 28 Jun 2017 07:24:07: 1000000 INFO @ Wed, 28 Jun 2017 07:24:14: 2000000 INFO @ Wed, 28 Jun 2017 07:24:17: 2000000 INFO @ Wed, 28 Jun 2017 07:24:17: 2000000 INFO @ Wed, 28 Jun 2017 07:24:23: 3000000 INFO @ Wed, 28 Jun 2017 07:24:27: 3000000 INFO @ Wed, 28 Jun 2017 07:24:27: 3000000 INFO @ Wed, 28 Jun 2017 07:24:34: 4000000 INFO @ Wed, 28 Jun 2017 07:24:36: 4000000 INFO @ Wed, 28 Jun 2017 07:24:38: 4000000 INFO @ Wed, 28 Jun 2017 07:24:44: 5000000 INFO @ Wed, 28 Jun 2017 07:24:44: 5000000 INFO @ Wed, 28 Jun 2017 07:24:48: 5000000 INFO @ Wed, 28 Jun 2017 07:24:53: 6000000 INFO @ Wed, 28 Jun 2017 07:24:54: 6000000 INFO @ Wed, 28 Jun 2017 07:24:58: 6000000 INFO @ Wed, 28 Jun 2017 07:25:01: 7000000 INFO @ Wed, 28 Jun 2017 07:25:04: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:25:04: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:25:04: #1 total tags in treatment: 3288654 INFO @ Wed, 28 Jun 2017 07:25:04: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:25:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 07:25:04: #1 tags after filtering in treatment: 2269787 INFO @ Wed, 28 Jun 2017 07:25:04: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 28 Jun 2017 07:25:04: #1 finished! INFO @ Wed, 28 Jun 2017 07:25:04: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:25:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:25:04: #2 number of paired peaks: 618 WARNING @ Wed, 28 Jun 2017 07:25:04: Fewer paired peaks (618) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 618 pairs to build model! INFO @ Wed, 28 Jun 2017 07:25:04: start model_add_line... INFO @ Wed, 28 Jun 2017 07:25:04: start X-correlation... INFO @ Wed, 28 Jun 2017 07:25:04: end of X-cor INFO @ Wed, 28 Jun 2017 07:25:04: #2 finished! INFO @ Wed, 28 Jun 2017 07:25:04: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:25:04: #2 alternative fragment length(s) may be 0,70,100,124,143,183,216,351,403,440,547,590 bps INFO @ Wed, 28 Jun 2017 07:25:04: #2.2 Generate R script for model : SRX1872741.10_model.r WARNING @ Wed, 28 Jun 2017 07:25:04: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:25:04: #2 You may need to consider one of the other alternative d(s): 0,70,100,124,143,183,216,351,403,440,547,590 WARNING @ Wed, 28 Jun 2017 07:25:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 07:25:04: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:25:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:25:05: 7000000 INFO @ Wed, 28 Jun 2017 07:25:07: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:25:07: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:25:07: #1 total tags in treatment: 3288654 INFO @ Wed, 28 Jun 2017 07:25:07: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:25:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 07:25:08: #1 tags after filtering in treatment: 2269787 INFO @ Wed, 28 Jun 2017 07:25:08: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 28 Jun 2017 07:25:08: #1 finished! INFO @ Wed, 28 Jun 2017 07:25:08: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:25:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:25:08: #2 number of paired peaks: 618 WARNING @ Wed, 28 Jun 2017 07:25:08: Fewer paired peaks (618) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 618 pairs to build model! INFO @ Wed, 28 Jun 2017 07:25:08: start model_add_line... INFO @ Wed, 28 Jun 2017 07:25:08: start X-correlation... INFO @ Wed, 28 Jun 2017 07:25:08: end of X-cor INFO @ Wed, 28 Jun 2017 07:25:08: #2 finished! INFO @ Wed, 28 Jun 2017 07:25:08: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:25:08: #2 alternative fragment length(s) may be 0,70,100,124,143,183,216,351,403,440,547,590 bps INFO @ Wed, 28 Jun 2017 07:25:08: #2.2 Generate R script for model : SRX1872741.05_model.r WARNING @ Wed, 28 Jun 2017 07:25:08: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:25:08: #2 You may need to consider one of the other alternative d(s): 0,70,100,124,143,183,216,351,403,440,547,590 WARNING @ Wed, 28 Jun 2017 07:25:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 07:25:08: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:25:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:25:09: 7000000 INFO @ Wed, 28 Jun 2017 07:25:11: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:25:11: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:25:11: #1 total tags in treatment: 3288654 INFO @ Wed, 28 Jun 2017 07:25:11: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:25:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 07:25:11: #1 tags after filtering in treatment: 2269787 INFO @ Wed, 28 Jun 2017 07:25:11: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 28 Jun 2017 07:25:11: #1 finished! INFO @ Wed, 28 Jun 2017 07:25:11: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:25:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:25:11: #2 number of paired peaks: 618 WARNING @ Wed, 28 Jun 2017 07:25:11: Fewer paired peaks (618) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 618 pairs to build model! INFO @ Wed, 28 Jun 2017 07:25:11: start model_add_line... INFO @ Wed, 28 Jun 2017 07:25:11: start X-correlation... INFO @ Wed, 28 Jun 2017 07:25:11: end of X-cor INFO @ Wed, 28 Jun 2017 07:25:11: #2 finished! INFO @ Wed, 28 Jun 2017 07:25:11: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 07:25:11: #2 alternative fragment length(s) may be 0,70,100,124,143,183,216,351,403,440,547,590 bps INFO @ Wed, 28 Jun 2017 07:25:11: #2.2 Generate R script for model : SRX1872741.20_model.r WARNING @ Wed, 28 Jun 2017 07:25:11: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:25:11: #2 You may need to consider one of the other alternative d(s): 0,70,100,124,143,183,216,351,403,440,547,590 WARNING @ Wed, 28 Jun 2017 07:25:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 07:25:11: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:25:11: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 ls: cannot access SRX1872741.05.bed: そのようなファイルやディレクトリはありません mv: cannot stat `SRX1872741.05.bed': そのようなファイルやディレクトリはありません /var/spool/uge/nt035i/job_scripts/9162302: line 231: 19698 終了しました MACS $i /var/spool/uge/nt035i/job_scripts/9162302: line 231: 19699 終了しました MACS $i /var/spool/uge/nt035i/job_scripts/9162302: line 231: 19700 終了しました MACS $i mv: cannot stat `SRX1872741.05.bb': そのようなファイルやディレクトリはありません ls: cannot access SRX1872741.10.bed: そのようなファイルやディレクトリはありません mv: cannot stat `SRX1872741.10.bed': そのようなファイルやディレクトリはありません mv: cannot stat `SRX1872741.10.bb': そのようなファイルやディレクトリはありません ls: cannot access SRX1872741.20.bed: そのようなファイルやディレクトリはありません mv: cannot stat `SRX1872741.20.bed': そのようなファイルやディレクトリはありません mv: cannot stat `SRX1872741.20.bb': そのようなファイルやディレクトリはありません