Job ID = 1293587 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T15:45:52 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T15:45:52 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra4/SRR/000345/SRR353683' 2019-06-02T15:46:02 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR353683', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 38,092,752 reads read : 38,092,752 reads written : 38,092,752 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory 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: 00:08:58 38092752 reads; of these: 38092752 (100.00%) were unpaired; of these: 10182755 (26.73%) aligned 0 times 22322089 (58.60%) aligned exactly 1 time 5587908 (14.67%) aligned >1 times 73.27% overall alignment rate Time searching: 00:08:58 Overall time: 00:08:58 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_sort_core] merging from 8 files... [bam_rmdupse_core] 16532045 / 27909997 = 0.5923 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, 03 Jun 2019 01:13:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.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 @ Mon, 03 Jun 2019 01:13:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:13:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:13:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.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 @ Mon, 03 Jun 2019 01:13:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:13:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:13:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.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 @ Mon, 03 Jun 2019 01:13:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:13:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:13:39: 1000000 INFO @ Mon, 03 Jun 2019 01:13:41: 1000000 INFO @ Mon, 03 Jun 2019 01:13:42: 1000000 INFO @ Mon, 03 Jun 2019 01:13:47: 2000000 INFO @ Mon, 03 Jun 2019 01:13:51: 2000000 INFO @ Mon, 03 Jun 2019 01:13:52: 2000000 INFO @ Mon, 03 Jun 2019 01:13:55: 3000000 INFO @ Mon, 03 Jun 2019 01:14:01: 3000000 INFO @ Mon, 03 Jun 2019 01:14:02: 3000000 INFO @ Mon, 03 Jun 2019 01:14:03: 4000000 INFO @ Mon, 03 Jun 2019 01:14:10: 5000000 INFO @ Mon, 03 Jun 2019 01:14:11: 4000000 INFO @ Mon, 03 Jun 2019 01:14:12: 4000000 INFO @ Mon, 03 Jun 2019 01:14:18: 6000000 INFO @ Mon, 03 Jun 2019 01:14:20: 5000000 INFO @ Mon, 03 Jun 2019 01:14:23: 5000000 INFO @ Mon, 03 Jun 2019 01:14:25: 7000000 INFO @ Mon, 03 Jun 2019 01:14:30: 6000000 INFO @ Mon, 03 Jun 2019 01:14:33: 6000000 INFO @ Mon, 03 Jun 2019 01:14:33: 8000000 INFO @ Mon, 03 Jun 2019 01:14:39: 7000000 INFO @ Mon, 03 Jun 2019 01:14:41: 9000000 INFO @ Mon, 03 Jun 2019 01:14:42: 7000000 INFO @ Mon, 03 Jun 2019 01:14:48: 10000000 INFO @ Mon, 03 Jun 2019 01:14:50: 8000000 INFO @ Mon, 03 Jun 2019 01:14:52: 8000000 INFO @ Mon, 03 Jun 2019 01:14:56: 11000000 INFO @ Mon, 03 Jun 2019 01:14:58: #1 tag size is determined as 41 bps INFO @ Mon, 03 Jun 2019 01:14:58: #1 tag size = 41 INFO @ Mon, 03 Jun 2019 01:14:58: #1 total tags in treatment: 11377952 INFO @ Mon, 03 Jun 2019 01:14:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:14:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:14:59: #1 tags after filtering in treatment: 11377952 INFO @ Mon, 03 Jun 2019 01:14:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:14:59: #1 finished! INFO @ Mon, 03 Jun 2019 01:14:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:14:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:15:00: #2 number of paired peaks: 142 WARNING @ Mon, 03 Jun 2019 01:15:00: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Mon, 03 Jun 2019 01:15:00: start model_add_line... INFO @ Mon, 03 Jun 2019 01:15:00: start X-correlation... INFO @ Mon, 03 Jun 2019 01:15:00: 9000000 INFO @ Mon, 03 Jun 2019 01:15:00: end of X-cor INFO @ Mon, 03 Jun 2019 01:15:00: #2 finished! INFO @ Mon, 03 Jun 2019 01:15:00: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 01:15:00: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 01:15:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.20_model.r WARNING @ Mon, 03 Jun 2019 01:15:00: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:15:00: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 01:15:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 01:15:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:15:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:15:01: 9000000 INFO @ Mon, 03 Jun 2019 01:15:09: 10000000 INFO @ Mon, 03 Jun 2019 01:15:10: 10000000 INFO @ Mon, 03 Jun 2019 01:15:19: 11000000 INFO @ Mon, 03 Jun 2019 01:15:20: 11000000 INFO @ Mon, 03 Jun 2019 01:15:22: #1 tag size is determined as 41 bps INFO @ Mon, 03 Jun 2019 01:15:22: #1 tag size = 41 INFO @ Mon, 03 Jun 2019 01:15:22: #1 total tags in treatment: 11377952 INFO @ Mon, 03 Jun 2019 01:15:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:15:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:15:22: #1 tags after filtering in treatment: 11377952 INFO @ Mon, 03 Jun 2019 01:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:15:22: #1 finished! INFO @ Mon, 03 Jun 2019 01:15:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:15:23: #1 tag size is determined as 41 bps INFO @ Mon, 03 Jun 2019 01:15:23: #1 tag size = 41 INFO @ Mon, 03 Jun 2019 01:15:23: #1 total tags in treatment: 11377952 INFO @ Mon, 03 Jun 2019 01:15:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:15:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 01:15:24: #1 tags after filtering in treatment: 11377952 INFO @ Mon, 03 Jun 2019 01:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:15:24: #1 finished! INFO @ Mon, 03 Jun 2019 01:15:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:15:24: #2 number of paired peaks: 142 WARNING @ Mon, 03 Jun 2019 01:15:24: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Mon, 03 Jun 2019 01:15:24: start model_add_line... INFO @ Mon, 03 Jun 2019 01:15:24: start X-correlation... INFO @ Mon, 03 Jun 2019 01:15:24: end of X-cor INFO @ Mon, 03 Jun 2019 01:15:24: #2 finished! INFO @ Mon, 03 Jun 2019 01:15:24: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 01:15:24: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 01:15:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.05_model.r WARNING @ Mon, 03 Jun 2019 01:15:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:15:24: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 01:15:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 01:15:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:15:25: #2 number of paired peaks: 142 WARNING @ Mon, 03 Jun 2019 01:15:25: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Mon, 03 Jun 2019 01:15:25: start model_add_line... INFO @ Mon, 03 Jun 2019 01:15:25: start X-correlation... INFO @ Mon, 03 Jun 2019 01:15:25: end of X-cor INFO @ Mon, 03 Jun 2019 01:15:25: #2 finished! INFO @ Mon, 03 Jun 2019 01:15:25: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 01:15:25: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 01:15:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.10_model.r WARNING @ Mon, 03 Jun 2019 01:15:25: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:15:25: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 01:15:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 01:15:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:15:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:15:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:15:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:15:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.20_summits.bed INFO @ Mon, 03 Jun 2019 01:15:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:15:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:15:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:16:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.05_summits.bed INFO @ Mon, 03 Jun 2019 01:16:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3067 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:16:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:16:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:16:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX101479/SRX101479.10_summits.bed INFO @ Mon, 03 Jun 2019 01:16:15: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1017 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。