Job ID = 10201990 sra ファイルのダウンロード中... Completed: 448686K bytes transferred in 14 seconds (262208K 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: SINGLE fastq に変換中... Written 19024370 spots for /home/okishinya/chipatlas/results/ce10/SRX2576659/SRR5272616.sra Written 19024370 spots total 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: 00:03:34 19024370 reads; of these: 19024370 (100.00%) were unpaired; of these: 147702 (0.78%) aligned 0 times 15659432 (82.31%) aligned exactly 1 time 3217236 (16.91%) aligned >1 times 99.22% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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 8 files... [bam_rmdupse_core] 1939215 / 18876668 = 0.1027 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 @ Mon, 13 Nov 2017 13:17:18: # Command line: callpeak -t SRX2576659.bam -f BAM -g ce -n SRX2576659.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576659.10 # format = BAM # ChIP-seq file = ['SRX2576659.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 @ Mon, 13 Nov 2017 13:17:18: # Command line: callpeak -t SRX2576659.bam -f BAM -g ce -n SRX2576659.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576659.05 # format = BAM # ChIP-seq file = ['SRX2576659.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 @ Mon, 13 Nov 2017 13:17:18: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:17:18: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:17:18: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:17:18: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:17:18: # Command line: callpeak -t SRX2576659.bam -f BAM -g ce -n SRX2576659.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576659.20 # format = BAM # ChIP-seq file = ['SRX2576659.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 @ Mon, 13 Nov 2017 13:17:18: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:17:18: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:17:25: 1000000 INFO @ Mon, 13 Nov 2017 13:17:26: 1000000 INFO @ Mon, 13 Nov 2017 13:17:26: 1000000 INFO @ Mon, 13 Nov 2017 13:17:32: 2000000 INFO @ Mon, 13 Nov 2017 13:17:33: 2000000 INFO @ Mon, 13 Nov 2017 13:17:33: 2000000 INFO @ Mon, 13 Nov 2017 13:17:39: 3000000 INFO @ Mon, 13 Nov 2017 13:17:40: 3000000 INFO @ Mon, 13 Nov 2017 13:17:40: 3000000 INFO @ Mon, 13 Nov 2017 13:17:46: 4000000 INFO @ Mon, 13 Nov 2017 13:17:47: 4000000 INFO @ Mon, 13 Nov 2017 13:17:47: 4000000 INFO @ Mon, 13 Nov 2017 13:17:53: 5000000 INFO @ Mon, 13 Nov 2017 13:17:54: 5000000 INFO @ Mon, 13 Nov 2017 13:17:55: 5000000 INFO @ Mon, 13 Nov 2017 13:18:00: 6000000 INFO @ Mon, 13 Nov 2017 13:18:01: 6000000 INFO @ Mon, 13 Nov 2017 13:18:02: 6000000 INFO @ Mon, 13 Nov 2017 13:18:06: 7000000 INFO @ Mon, 13 Nov 2017 13:18:08: 7000000 INFO @ Mon, 13 Nov 2017 13:18:10: 7000000 INFO @ Mon, 13 Nov 2017 13:18:13: 8000000 INFO @ Mon, 13 Nov 2017 13:18:16: 8000000 INFO @ Mon, 13 Nov 2017 13:18:17: 8000000 INFO @ Mon, 13 Nov 2017 13:18:20: 9000000 INFO @ Mon, 13 Nov 2017 13:18:23: 9000000 INFO @ Mon, 13 Nov 2017 13:18:25: 9000000 INFO @ Mon, 13 Nov 2017 13:18:27: 10000000 INFO @ Mon, 13 Nov 2017 13:18:30: 10000000 INFO @ Mon, 13 Nov 2017 13:18:32: 10000000 INFO @ Mon, 13 Nov 2017 13:18:34: 11000000 INFO @ Mon, 13 Nov 2017 13:18:38: 11000000 INFO @ Mon, 13 Nov 2017 13:18:40: 11000000 INFO @ Mon, 13 Nov 2017 13:18:41: 12000000 INFO @ Mon, 13 Nov 2017 13:18:45: 12000000 INFO @ Mon, 13 Nov 2017 13:18:47: 12000000 INFO @ Mon, 13 Nov 2017 13:18:47: 13000000 INFO @ Mon, 13 Nov 2017 13:18:52: 13000000 INFO @ Mon, 13 Nov 2017 13:18:54: 14000000 INFO @ Mon, 13 Nov 2017 13:18:55: 13000000 INFO @ Mon, 13 Nov 2017 13:19:00: 14000000 INFO @ Mon, 13 Nov 2017 13:19:01: 15000000 INFO @ Mon, 13 Nov 2017 13:19:02: 14000000 INFO @ Mon, 13 Nov 2017 13:19:07: 15000000 INFO @ Mon, 13 Nov 2017 13:19:08: 16000000 INFO @ Mon, 13 Nov 2017 13:19:09: 15000000 INFO @ Mon, 13 Nov 2017 13:19:14: 16000000 INFO @ Mon, 13 Nov 2017 13:19:14: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:19:14: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:19:14: #1 total tags in treatment: 16937453 INFO @ Mon, 13 Nov 2017 13:19:14: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:19:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:19:15: #1 tags after filtering in treatment: 16937453 INFO @ Mon, 13 Nov 2017 13:19:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:19:15: #1 finished! INFO @ Mon, 13 Nov 2017 13:19:15: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:19:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:19:16: #2 number of paired peaks: 199 WARNING @ Mon, 13 Nov 2017 13:19:16: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Mon, 13 Nov 2017 13:19:16: start model_add_line... INFO @ Mon, 13 Nov 2017 13:19:16: start X-correlation... INFO @ Mon, 13 Nov 2017 13:19:16: end of X-cor INFO @ Mon, 13 Nov 2017 13:19:16: #2 finished! INFO @ Mon, 13 Nov 2017 13:19:16: #2 predicted fragment length is 0 bps INFO @ Mon, 13 Nov 2017 13:19:16: #2 alternative fragment length(s) may be 0,30,65,472 bps INFO @ Mon, 13 Nov 2017 13:19:16: #2.2 Generate R script for model : SRX2576659.10_model.r WARNING @ Mon, 13 Nov 2017 13:19:16: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:19:16: #2 You may need to consider one of the other alternative d(s): 0,30,65,472 WARNING @ Mon, 13 Nov 2017 13:19:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:19:16: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:19:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:19:17: 16000000 INFO @ Mon, 13 Nov 2017 13:19:21: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:19:21: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:19:21: #1 total tags in treatment: 16937453 INFO @ Mon, 13 Nov 2017 13:19:21: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:19:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:19:21: #1 tags after filtering in treatment: 16937453 INFO @ Mon, 13 Nov 2017 13:19:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:19:21: #1 finished! INFO @ Mon, 13 Nov 2017 13:19:21: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:19:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:19:22: #2 number of paired peaks: 199 WARNING @ Mon, 13 Nov 2017 13:19:22: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Mon, 13 Nov 2017 13:19:22: start model_add_line... INFO @ Mon, 13 Nov 2017 13:19:22: start X-correlation... INFO @ Mon, 13 Nov 2017 13:19:22: end of X-cor INFO @ Mon, 13 Nov 2017 13:19:22: #2 finished! INFO @ Mon, 13 Nov 2017 13:19:22: #2 predicted fragment length is 0 bps INFO @ Mon, 13 Nov 2017 13:19:22: #2 alternative fragment length(s) may be 0,30,65,472 bps INFO @ Mon, 13 Nov 2017 13:19:22: #2.2 Generate R script for model : SRX2576659.05_model.r WARNING @ Mon, 13 Nov 2017 13:19:22: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:19:22: #2 You may need to consider one of the other alternative d(s): 0,30,65,472 WARNING @ Mon, 13 Nov 2017 13:19:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:19:22: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:19:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:19:24: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:19:24: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:19:24: #1 total tags in treatment: 16937453 INFO @ Mon, 13 Nov 2017 13:19:24: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:19:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:19:24: #1 tags after filtering in treatment: 16937453 INFO @ Mon, 13 Nov 2017 13:19:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:19:24: #1 finished! INFO @ Mon, 13 Nov 2017 13:19:24: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:19:25: #2 number of paired peaks: 199 WARNING @ Mon, 13 Nov 2017 13:19:25: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Mon, 13 Nov 2017 13:19:25: start model_add_line... INFO @ Mon, 13 Nov 2017 13:19:25: start X-correlation... INFO @ Mon, 13 Nov 2017 13:19:25: end of X-cor INFO @ Mon, 13 Nov 2017 13:19:25: #2 finished! INFO @ Mon, 13 Nov 2017 13:19:25: #2 predicted fragment length is 0 bps INFO @ Mon, 13 Nov 2017 13:19:25: #2 alternative fragment length(s) may be 0,30,65,472 bps INFO @ Mon, 13 Nov 2017 13:19:25: #2.2 Generate R script for model : SRX2576659.20_model.r WARNING @ Mon, 13 Nov 2017 13:19:25: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 13 Nov 2017 13:19:25: #2 You may need to consider one of the other alternative d(s): 0,30,65,472 WARNING @ Mon, 13 Nov 2017 13:19:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 13 Nov 2017 13:19:25: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:19:25: #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 SRX2576659.05.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 `SRX2576659.05.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/nt090i/job_scripts/10201990: line 253: 41571 終了しました MACS $i /var/spool/uge/nt090i/job_scripts/10201990: line 253: 41572 終了しました MACS $i /var/spool/uge/nt090i/job_scripts/10201990: line 253: 41574 終了しました MACS $i mv: cannot stat `SRX2576659.05.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 SRX2576659.10.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 `SRX2576659.10.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 `SRX2576659.10.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 SRX2576659.20.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 `SRX2576659.20.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 `SRX2576659.20.bb': そのようなファイルやディレクトリはありません