Job ID = 1294635 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:27:05 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 ) 2019-06-03T00:27:05 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 : 16,435,690 reads read : 16,435,690 reads written : 16,435,690 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: 00:08:22 16435690 reads; of these: 16435690 (100.00%) were unpaired; of these: 840634 (5.11%) aligned 0 times 11309662 (68.81%) aligned exactly 1 time 4285394 (26.07%) aligned >1 times 94.89% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 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] 2324963 / 15595056 = 0.1491 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 09:44:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.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 09:44:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:44:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:44:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.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 09:44:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:44:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:44:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.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 09:44:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:44:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:44:38: 1000000 INFO @ Mon, 03 Jun 2019 09:44:38: 1000000 INFO @ Mon, 03 Jun 2019 09:44:39: 1000000 INFO @ Mon, 03 Jun 2019 09:44:46: 2000000 INFO @ Mon, 03 Jun 2019 09:44:46: 2000000 INFO @ Mon, 03 Jun 2019 09:44:49: 2000000 INFO @ Mon, 03 Jun 2019 09:44:55: 3000000 INFO @ Mon, 03 Jun 2019 09:44:55: 3000000 INFO @ Mon, 03 Jun 2019 09:44:59: 3000000 INFO @ Mon, 03 Jun 2019 09:45:04: 4000000 INFO @ Mon, 03 Jun 2019 09:45:04: 4000000 INFO @ Mon, 03 Jun 2019 09:45:09: 4000000 INFO @ Mon, 03 Jun 2019 09:45:12: 5000000 INFO @ Mon, 03 Jun 2019 09:45:12: 5000000 INFO @ Mon, 03 Jun 2019 09:45:18: 5000000 INFO @ Mon, 03 Jun 2019 09:45:20: 6000000 INFO @ Mon, 03 Jun 2019 09:45:21: 6000000 INFO @ Mon, 03 Jun 2019 09:45:28: 6000000 INFO @ Mon, 03 Jun 2019 09:45:28: 7000000 INFO @ Mon, 03 Jun 2019 09:45:29: 7000000 INFO @ Mon, 03 Jun 2019 09:45:37: 8000000 INFO @ Mon, 03 Jun 2019 09:45:37: 8000000 INFO @ Mon, 03 Jun 2019 09:45:37: 7000000 INFO @ Mon, 03 Jun 2019 09:45:45: 9000000 INFO @ Mon, 03 Jun 2019 09:45:45: 9000000 INFO @ Mon, 03 Jun 2019 09:45:47: 8000000 INFO @ Mon, 03 Jun 2019 09:45:53: 10000000 INFO @ Mon, 03 Jun 2019 09:45:53: 10000000 INFO @ Mon, 03 Jun 2019 09:45:56: 9000000 INFO @ Mon, 03 Jun 2019 09:46:01: 11000000 INFO @ Mon, 03 Jun 2019 09:46:02: 11000000 INFO @ Mon, 03 Jun 2019 09:46:06: 10000000 INFO @ Mon, 03 Jun 2019 09:46:10: 12000000 INFO @ Mon, 03 Jun 2019 09:46:11: 12000000 INFO @ Mon, 03 Jun 2019 09:46:16: 11000000 INFO @ Mon, 03 Jun 2019 09:46:19: 13000000 INFO @ Mon, 03 Jun 2019 09:46:19: 13000000 INFO @ Mon, 03 Jun 2019 09:46:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:46:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:46:21: #1 total tags in treatment: 13270093 INFO @ Mon, 03 Jun 2019 09:46:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:46:21: #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 09:46:21: #1 tags after filtering in treatment: 13270093 INFO @ Mon, 03 Jun 2019 09:46:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:46:21: #1 finished! INFO @ Mon, 03 Jun 2019 09:46:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:46:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:46:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:46:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:46:21: #1 total tags in treatment: 13270093 INFO @ Mon, 03 Jun 2019 09:46:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:46:21: #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 09:46:22: #1 tags after filtering in treatment: 13270093 INFO @ Mon, 03 Jun 2019 09:46:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:46:22: #1 finished! INFO @ Mon, 03 Jun 2019 09:46:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:46:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:46:22: #2 number of paired peaks: 335 WARNING @ Mon, 03 Jun 2019 09:46:22: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Mon, 03 Jun 2019 09:46:22: start model_add_line... INFO @ Mon, 03 Jun 2019 09:46:22: start X-correlation... INFO @ Mon, 03 Jun 2019 09:46:22: end of X-cor INFO @ Mon, 03 Jun 2019 09:46:22: #2 finished! INFO @ Mon, 03 Jun 2019 09:46:22: #2 predicted fragment length is 40 bps INFO @ Mon, 03 Jun 2019 09:46:22: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 03 Jun 2019 09:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.10_model.r WARNING @ Mon, 03 Jun 2019 09:46:22: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:46:22: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 03 Jun 2019 09:46:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 09:46:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:46:23: #2 number of paired peaks: 335 WARNING @ Mon, 03 Jun 2019 09:46:23: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Mon, 03 Jun 2019 09:46:23: start model_add_line... INFO @ Mon, 03 Jun 2019 09:46:23: start X-correlation... INFO @ Mon, 03 Jun 2019 09:46:23: end of X-cor INFO @ Mon, 03 Jun 2019 09:46:23: #2 finished! INFO @ Mon, 03 Jun 2019 09:46:23: #2 predicted fragment length is 40 bps INFO @ Mon, 03 Jun 2019 09:46:23: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 03 Jun 2019 09:46:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.05_model.r WARNING @ Mon, 03 Jun 2019 09:46:23: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:46:23: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 03 Jun 2019 09:46:23: #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 09:46:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:46:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:46:26: 12000000 INFO @ Mon, 03 Jun 2019 09:46:35: 13000000 INFO @ Mon, 03 Jun 2019 09:46:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:46:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:46:37: #1 total tags in treatment: 13270093 INFO @ Mon, 03 Jun 2019 09:46:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:46:37: #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 09:46:38: #1 tags after filtering in treatment: 13270093 INFO @ Mon, 03 Jun 2019 09:46:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:46:38: #1 finished! INFO @ Mon, 03 Jun 2019 09:46:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:46:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:46:39: #2 number of paired peaks: 335 WARNING @ Mon, 03 Jun 2019 09:46:39: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Mon, 03 Jun 2019 09:46:39: start model_add_line... INFO @ Mon, 03 Jun 2019 09:46:39: start X-correlation... INFO @ Mon, 03 Jun 2019 09:46:39: end of X-cor INFO @ Mon, 03 Jun 2019 09:46:39: #2 finished! INFO @ Mon, 03 Jun 2019 09:46:39: #2 predicted fragment length is 40 bps INFO @ Mon, 03 Jun 2019 09:46:39: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 03 Jun 2019 09:46:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.20_model.r WARNING @ Mon, 03 Jun 2019 09:46:39: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:46:39: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 03 Jun 2019 09:46:39: #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 09:46:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:46:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:46:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:46:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:47:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:47:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:47:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:47:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.10_summits.bed INFO @ Mon, 03 Jun 2019 09:47:16: Done! INFO @ Mon, 03 Jun 2019 09:47:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:47:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:47:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.05_summits.bed pass1 - making usageList (9 chroms): 1 millis INFO @ Mon, 03 Jun 2019 09:47:16: Done! pass2 - checking and writing primary data (1573 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1972 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:47:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:47:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:47:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287795/SRX287795.20_summits.bed INFO @ Mon, 03 Jun 2019 09:47:31: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1144 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。