Job ID = 1293659 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:26:05 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 41,315,553 reads read : 41,315,553 reads written : 41,315,553 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: 00:12:37 41315553 reads; of these: 41315553 (100.00%) were unpaired; of these: 3499231 (8.47%) aligned 0 times 30452578 (73.71%) aligned exactly 1 time 7363744 (17.82%) aligned >1 times 91.53% overall alignment rate Time searching: 00:12:37 Overall time: 00:12:37 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 12 files... [bam_rmdupse_core] 17506405 / 37816322 = 0.4629 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 02:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.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 02:00:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:00:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.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 02:00:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:00:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.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 02:00:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:00:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:00:15: 1000000 INFO @ Mon, 03 Jun 2019 02:00:18: 1000000 INFO @ Mon, 03 Jun 2019 02:00:18: 1000000 INFO @ Mon, 03 Jun 2019 02:00:22: 2000000 INFO @ Mon, 03 Jun 2019 02:00:28: 2000000 INFO @ Mon, 03 Jun 2019 02:00:28: 2000000 INFO @ Mon, 03 Jun 2019 02:00:29: 3000000 INFO @ Mon, 03 Jun 2019 02:00:36: 4000000 INFO @ Mon, 03 Jun 2019 02:00:38: 3000000 INFO @ Mon, 03 Jun 2019 02:00:38: 3000000 INFO @ Mon, 03 Jun 2019 02:00:43: 5000000 INFO @ Mon, 03 Jun 2019 02:00:49: 4000000 INFO @ Mon, 03 Jun 2019 02:00:49: 4000000 INFO @ Mon, 03 Jun 2019 02:00:50: 6000000 INFO @ Mon, 03 Jun 2019 02:00:58: 7000000 INFO @ Mon, 03 Jun 2019 02:01:01: 5000000 INFO @ Mon, 03 Jun 2019 02:01:01: 5000000 INFO @ Mon, 03 Jun 2019 02:01:05: 8000000 INFO @ Mon, 03 Jun 2019 02:01:11: 6000000 INFO @ Mon, 03 Jun 2019 02:01:11: 6000000 INFO @ Mon, 03 Jun 2019 02:01:12: 9000000 INFO @ Mon, 03 Jun 2019 02:01:19: 10000000 INFO @ Mon, 03 Jun 2019 02:01:21: 7000000 INFO @ Mon, 03 Jun 2019 02:01:21: 7000000 INFO @ Mon, 03 Jun 2019 02:01:26: 11000000 INFO @ Mon, 03 Jun 2019 02:01:30: 8000000 INFO @ Mon, 03 Jun 2019 02:01:31: 8000000 INFO @ Mon, 03 Jun 2019 02:01:33: 12000000 INFO @ Mon, 03 Jun 2019 02:01:39: 9000000 INFO @ Mon, 03 Jun 2019 02:01:40: 13000000 INFO @ Mon, 03 Jun 2019 02:01:41: 9000000 INFO @ Mon, 03 Jun 2019 02:01:47: 14000000 INFO @ Mon, 03 Jun 2019 02:01:49: 10000000 INFO @ Mon, 03 Jun 2019 02:01:51: 10000000 INFO @ Mon, 03 Jun 2019 02:01:55: 15000000 INFO @ Mon, 03 Jun 2019 02:01:58: 11000000 INFO @ Mon, 03 Jun 2019 02:02:01: 11000000 INFO @ Mon, 03 Jun 2019 02:02:02: 16000000 INFO @ Mon, 03 Jun 2019 02:02:07: 12000000 INFO @ Mon, 03 Jun 2019 02:02:09: 17000000 INFO @ Mon, 03 Jun 2019 02:02:11: 12000000 INFO @ Mon, 03 Jun 2019 02:02:16: 18000000 INFO @ Mon, 03 Jun 2019 02:02:17: 13000000 INFO @ Mon, 03 Jun 2019 02:02:21: 13000000 INFO @ Mon, 03 Jun 2019 02:02:23: 19000000 INFO @ Mon, 03 Jun 2019 02:02:26: 14000000 INFO @ Mon, 03 Jun 2019 02:02:30: 20000000 INFO @ Mon, 03 Jun 2019 02:02:30: 14000000 INFO @ Mon, 03 Jun 2019 02:02:32: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 02:02:32: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 02:02:32: #1 total tags in treatment: 20309917 INFO @ Mon, 03 Jun 2019 02:02:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:02:32: #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 02:02:33: #1 tags after filtering in treatment: 20309917 INFO @ Mon, 03 Jun 2019 02:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:02:33: #1 finished! INFO @ Mon, 03 Jun 2019 02:02:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:02:35: #2 number of paired peaks: 103 WARNING @ Mon, 03 Jun 2019 02:02:35: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Mon, 03 Jun 2019 02:02:35: start model_add_line... INFO @ Mon, 03 Jun 2019 02:02:35: start X-correlation... INFO @ Mon, 03 Jun 2019 02:02:35: end of X-cor INFO @ Mon, 03 Jun 2019 02:02:35: #2 finished! INFO @ Mon, 03 Jun 2019 02:02:35: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 02:02:35: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 03 Jun 2019 02:02:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.20_model.r WARNING @ Mon, 03 Jun 2019 02:02:35: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:02:35: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 03 Jun 2019 02:02:35: #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 02:02:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:02:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:02:35: 15000000 INFO @ Mon, 03 Jun 2019 02:02:40: 15000000 INFO @ Mon, 03 Jun 2019 02:02:45: 16000000 INFO @ Mon, 03 Jun 2019 02:02:50: 16000000 INFO @ Mon, 03 Jun 2019 02:02:55: 17000000 INFO @ Mon, 03 Jun 2019 02:03:00: 17000000 INFO @ Mon, 03 Jun 2019 02:03:05: 18000000 INFO @ Mon, 03 Jun 2019 02:03:10: 18000000 INFO @ Mon, 03 Jun 2019 02:03:14: 19000000 INFO @ Mon, 03 Jun 2019 02:03:19: 19000000 INFO @ Mon, 03 Jun 2019 02:03:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:03:24: 20000000 INFO @ Mon, 03 Jun 2019 02:03:27: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 02:03:27: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 02:03:27: #1 total tags in treatment: 20309917 INFO @ Mon, 03 Jun 2019 02:03:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:03:27: #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 02:03:28: #1 tags after filtering in treatment: 20309917 INFO @ Mon, 03 Jun 2019 02:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:03:28: #1 finished! INFO @ Mon, 03 Jun 2019 02:03:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:03:29: 20000000 INFO @ Mon, 03 Jun 2019 02:03:30: #2 number of paired peaks: 103 WARNING @ Mon, 03 Jun 2019 02:03:30: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Mon, 03 Jun 2019 02:03:30: start model_add_line... INFO @ Mon, 03 Jun 2019 02:03:30: start X-correlation... INFO @ Mon, 03 Jun 2019 02:03:30: end of X-cor INFO @ Mon, 03 Jun 2019 02:03:30: #2 finished! INFO @ Mon, 03 Jun 2019 02:03:30: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 02:03:30: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 03 Jun 2019 02:03:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.10_model.r WARNING @ Mon, 03 Jun 2019 02:03:30: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:03:30: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 03 Jun 2019 02:03:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 02:03:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:03:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:03:31: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 02:03:31: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 02:03:31: #1 total tags in treatment: 20309917 INFO @ Mon, 03 Jun 2019 02:03:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:03:31: #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 02:03:32: #1 tags after filtering in treatment: 20309917 INFO @ Mon, 03 Jun 2019 02:03:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:03:32: #1 finished! INFO @ Mon, 03 Jun 2019 02:03:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:03:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:03:34: #2 number of paired peaks: 103 WARNING @ Mon, 03 Jun 2019 02:03:34: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Mon, 03 Jun 2019 02:03:34: start model_add_line... INFO @ Mon, 03 Jun 2019 02:03:34: start X-correlation... INFO @ Mon, 03 Jun 2019 02:03:34: end of X-cor INFO @ Mon, 03 Jun 2019 02:03:34: #2 finished! INFO @ Mon, 03 Jun 2019 02:03:34: #2 predicted fragment length is 34 bps INFO @ Mon, 03 Jun 2019 02:03:34: #2 alternative fragment length(s) may be 34 bps INFO @ Mon, 03 Jun 2019 02:03:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.05_model.r WARNING @ Mon, 03 Jun 2019 02:03:34: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:03:34: #2 You may need to consider one of the other alternative d(s): 34 WARNING @ Mon, 03 Jun 2019 02:03:34: #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 02:03:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:03:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:03:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:03:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:03:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.20_summits.bed INFO @ Mon, 03 Jun 2019 02:03:49: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (985 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:04:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:04:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:04:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:04:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:04:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.10_summits.bed INFO @ Mon, 03 Jun 2019 02:04:44: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1520 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:04:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:04:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:04:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104971/SRX104971.05_summits.bed INFO @ Mon, 03 Jun 2019 02:04:47: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2370 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。