Job ID = 1294700 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:37:57 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 ) 2019-06-03T00:38:02 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 ) 2019-06-03T00:41:44 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 ) 2019-06-03T00:42:16 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 ) 2019-06-03T00:46:11 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 : 13,809,114 reads read : 13,809,114 reads written : 13,809,114 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: 00:06:32 13809114 reads; of these: 13809114 (100.00%) were unpaired; of these: 547964 (3.97%) aligned 0 times 8994241 (65.13%) aligned exactly 1 time 4266909 (30.90%) aligned >1 times 96.03% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1851591 / 13261150 = 0.1396 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 09:57:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.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 09:57:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:57:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:57:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.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 09:57:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:57:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:57:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.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 09:57:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:57:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:57:51: 1000000 INFO @ Mon, 03 Jun 2019 09:57:51: 1000000 INFO @ Mon, 03 Jun 2019 09:57:53: 1000000 INFO @ Mon, 03 Jun 2019 09:57:58: 2000000 INFO @ Mon, 03 Jun 2019 09:58:00: 2000000 INFO @ Mon, 03 Jun 2019 09:58:03: 2000000 INFO @ Mon, 03 Jun 2019 09:58:06: 3000000 INFO @ Mon, 03 Jun 2019 09:58:09: 3000000 INFO @ Mon, 03 Jun 2019 09:58:13: 3000000 INFO @ Mon, 03 Jun 2019 09:58:14: 4000000 INFO @ Mon, 03 Jun 2019 09:58:18: 4000000 INFO @ Mon, 03 Jun 2019 09:58:22: 5000000 INFO @ Mon, 03 Jun 2019 09:58:23: 4000000 INFO @ Mon, 03 Jun 2019 09:58:27: 5000000 INFO @ Mon, 03 Jun 2019 09:58:29: 6000000 INFO @ Mon, 03 Jun 2019 09:58:33: 5000000 INFO @ Mon, 03 Jun 2019 09:58:36: 6000000 INFO @ Mon, 03 Jun 2019 09:58:37: 7000000 INFO @ Mon, 03 Jun 2019 09:58:43: 6000000 INFO @ Mon, 03 Jun 2019 09:58:44: 7000000 INFO @ Mon, 03 Jun 2019 09:58:44: 8000000 INFO @ Mon, 03 Jun 2019 09:58:52: 9000000 INFO @ Mon, 03 Jun 2019 09:58:53: 8000000 INFO @ Mon, 03 Jun 2019 09:58:53: 7000000 INFO @ Mon, 03 Jun 2019 09:59:00: 10000000 INFO @ Mon, 03 Jun 2019 09:59:01: 9000000 INFO @ Mon, 03 Jun 2019 09:59:03: 8000000 INFO @ Mon, 03 Jun 2019 09:59:07: 11000000 INFO @ Mon, 03 Jun 2019 09:59:10: 10000000 INFO @ Mon, 03 Jun 2019 09:59:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:59:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:59:10: #1 total tags in treatment: 11409559 INFO @ Mon, 03 Jun 2019 09:59:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:59:10: #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 09:59:11: #1 tags after filtering in treatment: 11409559 INFO @ Mon, 03 Jun 2019 09:59:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:59:11: #1 finished! INFO @ Mon, 03 Jun 2019 09:59:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:59:12: #2 number of paired peaks: 438 WARNING @ Mon, 03 Jun 2019 09:59:12: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Mon, 03 Jun 2019 09:59:12: start model_add_line... INFO @ Mon, 03 Jun 2019 09:59:12: start X-correlation... INFO @ Mon, 03 Jun 2019 09:59:12: end of X-cor INFO @ Mon, 03 Jun 2019 09:59:12: #2 finished! INFO @ Mon, 03 Jun 2019 09:59:12: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 09:59:12: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 09:59:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.05_model.r WARNING @ Mon, 03 Jun 2019 09:59:12: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:59:12: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 09:59:12: #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 09:59:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:59:13: 9000000 INFO @ Mon, 03 Jun 2019 09:59:19: 11000000 INFO @ Mon, 03 Jun 2019 09:59:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:59:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:59:22: #1 total tags in treatment: 11409559 INFO @ Mon, 03 Jun 2019 09:59:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:59:22: #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 09:59:22: 10000000 INFO @ Mon, 03 Jun 2019 09:59:23: #1 tags after filtering in treatment: 11409559 INFO @ Mon, 03 Jun 2019 09:59:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:59:23: #1 finished! INFO @ Mon, 03 Jun 2019 09:59:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:59:24: #2 number of paired peaks: 438 WARNING @ Mon, 03 Jun 2019 09:59:24: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Mon, 03 Jun 2019 09:59:24: start model_add_line... INFO @ Mon, 03 Jun 2019 09:59:24: start X-correlation... INFO @ Mon, 03 Jun 2019 09:59:24: end of X-cor INFO @ Mon, 03 Jun 2019 09:59:24: #2 finished! INFO @ Mon, 03 Jun 2019 09:59:24: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 09:59:24: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 09:59:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.20_model.r WARNING @ Mon, 03 Jun 2019 09:59:24: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:59:24: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 09:59:24: #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 09:59:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:59:32: 11000000 INFO @ Mon, 03 Jun 2019 09:59:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:59:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:59:36: #1 total tags in treatment: 11409559 INFO @ Mon, 03 Jun 2019 09:59:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:59:36: #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 09:59:36: #1 tags after filtering in treatment: 11409559 INFO @ Mon, 03 Jun 2019 09:59:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:59:36: #1 finished! INFO @ Mon, 03 Jun 2019 09:59:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:59:37: #2 number of paired peaks: 438 WARNING @ Mon, 03 Jun 2019 09:59:37: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Mon, 03 Jun 2019 09:59:37: start model_add_line... INFO @ Mon, 03 Jun 2019 09:59:37: start X-correlation... INFO @ Mon, 03 Jun 2019 09:59:37: end of X-cor INFO @ Mon, 03 Jun 2019 09:59:37: #2 finished! INFO @ Mon, 03 Jun 2019 09:59:37: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 09:59:37: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 09:59:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.10_model.r WARNING @ Mon, 03 Jun 2019 09:59:37: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:59:37: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 09:59:37: #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 09:59:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:59:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:59:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:59:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:59:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:59:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.05_summits.bed INFO @ Mon, 03 Jun 2019 09:59:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2101 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:00:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:00:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:00:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:00:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.20_summits.bed INFO @ Mon, 03 Jun 2019 10:00:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1404 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:00:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:00:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:00:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287829/SRX287829.10_summits.bed INFO @ Mon, 03 Jun 2019 10:00:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1844 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。