Job ID = 11634698 sra ファイルのダウンロード中... Completed: 787942K bytes transferred in 10 seconds (602004K 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... Read 23340924 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4940194/SRR8113809.sra Written 23340924 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4940194/SRR8113809.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 Warning: skipping read 'SRR8113809.2720144 2720144 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.2720144 2720144 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.3497198 3497198 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.3497198 3497198 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.3697182 3697182 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.3697182 3697182 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.4621303 4621303 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.4621303 4621303 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.5630754 5630754 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.5630754 5630754 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.5959922 5959922 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.5959922 5959922 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.11530201 11530201 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.11530201 11530201 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.11817962 11817962 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.11817962 11817962 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.14180624 14180624 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.14180624 14180624 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.14180635 14180635 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.14180635 14180635 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.15651593 15651593 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.15651593 15651593 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.16054010 16054010 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.16054010 16054010 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.17190772 17190772 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.17190772 17190772 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.19513980 19513980 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.19513980 19513980 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.20624584 20624584 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.20624584 20624584 length=1' because it was < 2 characters long Warning: skipping read 'SRR8113809.21351200 21351200 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR8113809.21351200 21351200 length=1' because it was < 2 characters long Multiseed full-index search: 00:05:32 23340924 reads; of these: 23340924 (100.00%) were unpaired; of these: 2495831 (10.69%) aligned 0 times 18676428 (80.02%) aligned exactly 1 time 2168665 (9.29%) aligned >1 times 89.31% 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_sort_core] merging from 12 files... [bam_rmdupse_core] 13962641 / 20845093 = 0.6698 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 @ Fri, 15 Feb 2019 10:39:45: # Command line: callpeak -t SRX4940194.bam -f BAM -g 12100000 -n SRX4940194.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4940194.05 # format = BAM # ChIP-seq file = ['SRX4940194.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 @ Fri, 15 Feb 2019 10:39:45: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:39:45: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:39:45: # Command line: callpeak -t SRX4940194.bam -f BAM -g 12100000 -n SRX4940194.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4940194.20 # format = BAM # ChIP-seq file = ['SRX4940194.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 @ Fri, 15 Feb 2019 10:39:45: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:39:45: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:39:45: # Command line: callpeak -t SRX4940194.bam -f BAM -g 12100000 -n SRX4940194.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4940194.10 # format = BAM # ChIP-seq file = ['SRX4940194.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 @ Fri, 15 Feb 2019 10:39:45: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:39:45: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:39:52: 1000000 INFO @ Fri, 15 Feb 2019 10:39:52: 1000000 INFO @ Fri, 15 Feb 2019 10:39:52: 1000000 INFO @ Fri, 15 Feb 2019 10:40:00: 2000000 INFO @ Fri, 15 Feb 2019 10:40:00: 2000000 INFO @ Fri, 15 Feb 2019 10:40:00: 2000000 INFO @ Fri, 15 Feb 2019 10:40:07: 3000000 INFO @ Fri, 15 Feb 2019 10:40:08: 3000000 INFO @ Fri, 15 Feb 2019 10:40:08: 3000000 INFO @ Fri, 15 Feb 2019 10:40:15: 4000000 INFO @ Fri, 15 Feb 2019 10:40:15: 4000000 INFO @ Fri, 15 Feb 2019 10:40:15: 4000000 INFO @ Fri, 15 Feb 2019 10:40:22: 5000000 INFO @ Fri, 15 Feb 2019 10:40:23: 5000000 INFO @ Fri, 15 Feb 2019 10:40:23: 5000000 INFO @ Fri, 15 Feb 2019 10:40:30: 6000000 INFO @ Fri, 15 Feb 2019 10:40:30: 6000000 INFO @ Fri, 15 Feb 2019 10:40:30: 6000000 INFO @ Fri, 15 Feb 2019 10:40:36: #1 tag size is determined as 65 bps INFO @ Fri, 15 Feb 2019 10:40:36: #1 tag size = 65 INFO @ Fri, 15 Feb 2019 10:40:36: #1 total tags in treatment: 6882452 INFO @ Fri, 15 Feb 2019 10:40:36: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:40:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:40:36: #1 tags after filtering in treatment: 6882452 INFO @ Fri, 15 Feb 2019 10:40:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:40:36: #1 finished! INFO @ Fri, 15 Feb 2019 10:40:36: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:40:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:40:37: #1 tag size is determined as 65 bps INFO @ Fri, 15 Feb 2019 10:40:37: #1 tag size = 65 INFO @ Fri, 15 Feb 2019 10:40:37: #1 total tags in treatment: 6882452 INFO @ Fri, 15 Feb 2019 10:40:37: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:40:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:40:37: #1 tags after filtering in treatment: 6882452 INFO @ Fri, 15 Feb 2019 10:40:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:40:37: #1 finished! INFO @ Fri, 15 Feb 2019 10:40:37: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:40:37: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:40:37: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 15 Feb 2019 10:40:37: Process for pairing-model is terminated! cat: SRX4940194.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Fri, 15 Feb 2019 10:40:37: #1 tag size is determined as 65 bps INFO @ Fri, 15 Feb 2019 10:40:37: #1 tag size = 65 INFO @ Fri, 15 Feb 2019 10:40:37: #1 total tags in treatment: 6882452 INFO @ Fri, 15 Feb 2019 10:40:37: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:40:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4940194.20_model.r': 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 `SRX4940194.20_*.xls': 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 `SRX4940194.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 10:40:37: #1 tags after filtering in treatment: 6882452 INFO @ Fri, 15 Feb 2019 10:40:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:40:37: #1 finished! INFO @ Fri, 15 Feb 2019 10:40:37: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:40:37: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:40:37: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 15 Feb 2019 10:40:37: Process for pairing-model is terminated! cat: SRX4940194.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4940194.05_model.r': 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 `SRX4940194.05_*.xls': 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 `SRX4940194.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 10:40:37: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:40:37: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 15 Feb 2019 10:40:37: Process for pairing-model is terminated! cat: SRX4940194.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 9 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4940194.10_model.r': 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 `SRX4940194.10_*.xls': 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 `SRX4940194.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。