Job ID = 1307517 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:22:46 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 ) 2019-06-03T13:26:16 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 ) 2019-06-03T13:26:16 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 ) 2019-06-03T13:27:34 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 ) 2019-06-03T13:27:34 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 : 28,775,089 reads read : 57,550,178 reads written : 28,775,089 reads 0-length : 28,775,089 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: 00:15:22 28775089 reads; of these: 28775089 (100.00%) were unpaired; of these: 1384211 (4.81%) aligned 0 times 18666698 (64.87%) aligned exactly 1 time 8724180 (30.32%) aligned >1 times 95.19% overall alignment rate Time searching: 00:15:22 Overall time: 00:15:22 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 12 files... [bam_rmdupse_core] 3626387 / 27390878 = 0.1324 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 22:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.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 22:57:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:57:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.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 22:57:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:57:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.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 22:57:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:57:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:57:34: 1000000 INFO @ Mon, 03 Jun 2019 22:57:35: 1000000 INFO @ Mon, 03 Jun 2019 22:57:35: 1000000 INFO @ Mon, 03 Jun 2019 22:57:44: 2000000 INFO @ Mon, 03 Jun 2019 22:57:44: 2000000 INFO @ Mon, 03 Jun 2019 22:57:46: 2000000 INFO @ Mon, 03 Jun 2019 22:57:53: 3000000 INFO @ Mon, 03 Jun 2019 22:57:53: 3000000 INFO @ Mon, 03 Jun 2019 22:57:56: 3000000 INFO @ Mon, 03 Jun 2019 22:58:02: 4000000 INFO @ Mon, 03 Jun 2019 22:58:02: 4000000 INFO @ Mon, 03 Jun 2019 22:58:06: 4000000 INFO @ Mon, 03 Jun 2019 22:58:11: 5000000 INFO @ Mon, 03 Jun 2019 22:58:11: 5000000 INFO @ Mon, 03 Jun 2019 22:58:15: 5000000 INFO @ Mon, 03 Jun 2019 22:58:19: 6000000 INFO @ Mon, 03 Jun 2019 22:58:20: 6000000 INFO @ Mon, 03 Jun 2019 22:58:25: 6000000 INFO @ Mon, 03 Jun 2019 22:58:28: 7000000 INFO @ Mon, 03 Jun 2019 22:58:29: 7000000 INFO @ Mon, 03 Jun 2019 22:58:36: 7000000 INFO @ Mon, 03 Jun 2019 22:58:37: 8000000 INFO @ Mon, 03 Jun 2019 22:58:37: 8000000 INFO @ Mon, 03 Jun 2019 22:58:46: 9000000 INFO @ Mon, 03 Jun 2019 22:58:46: 8000000 INFO @ Mon, 03 Jun 2019 22:58:46: 9000000 INFO @ Mon, 03 Jun 2019 22:58:54: 10000000 INFO @ Mon, 03 Jun 2019 22:58:55: 10000000 INFO @ Mon, 03 Jun 2019 22:58:55: 9000000 INFO @ Mon, 03 Jun 2019 22:59:03: 11000000 INFO @ Mon, 03 Jun 2019 22:59:04: 11000000 INFO @ Mon, 03 Jun 2019 22:59:05: 10000000 INFO @ Mon, 03 Jun 2019 22:59:12: 12000000 INFO @ Mon, 03 Jun 2019 22:59:12: 12000000 INFO @ Mon, 03 Jun 2019 22:59:16: 11000000 INFO @ Mon, 03 Jun 2019 22:59:21: 13000000 INFO @ Mon, 03 Jun 2019 22:59:21: 13000000 INFO @ Mon, 03 Jun 2019 22:59:26: 12000000 INFO @ Mon, 03 Jun 2019 22:59:30: 14000000 INFO @ Mon, 03 Jun 2019 22:59:30: 14000000 INFO @ Mon, 03 Jun 2019 22:59:36: 13000000 INFO @ Mon, 03 Jun 2019 22:59:39: 15000000 INFO @ Mon, 03 Jun 2019 22:59:39: 15000000 INFO @ Mon, 03 Jun 2019 22:59:46: 14000000 INFO @ Mon, 03 Jun 2019 22:59:48: 16000000 INFO @ Mon, 03 Jun 2019 22:59:48: 16000000 INFO @ Mon, 03 Jun 2019 22:59:55: 15000000 INFO @ Mon, 03 Jun 2019 22:59:57: 17000000 INFO @ Mon, 03 Jun 2019 22:59:57: 17000000 INFO @ Mon, 03 Jun 2019 23:00:05: 16000000 INFO @ Mon, 03 Jun 2019 23:00:06: 18000000 INFO @ Mon, 03 Jun 2019 23:00:06: 18000000 INFO @ Mon, 03 Jun 2019 23:00:14: 17000000 INFO @ Mon, 03 Jun 2019 23:00:14: 19000000 INFO @ Mon, 03 Jun 2019 23:00:15: 19000000 INFO @ Mon, 03 Jun 2019 23:00:24: 20000000 INFO @ Mon, 03 Jun 2019 23:00:24: 18000000 INFO @ Mon, 03 Jun 2019 23:00:24: 20000000 INFO @ Mon, 03 Jun 2019 23:00:33: 21000000 INFO @ Mon, 03 Jun 2019 23:00:33: 21000000 INFO @ Mon, 03 Jun 2019 23:00:34: 19000000 INFO @ Mon, 03 Jun 2019 23:00:42: 22000000 INFO @ Mon, 03 Jun 2019 23:00:43: 22000000 INFO @ Mon, 03 Jun 2019 23:00:46: 20000000 INFO @ Mon, 03 Jun 2019 23:00:51: 23000000 INFO @ Mon, 03 Jun 2019 23:00:52: 23000000 INFO @ Mon, 03 Jun 2019 23:00:56: 21000000 INFO @ Mon, 03 Jun 2019 23:00:59: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:00:59: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:00:59: #1 total tags in treatment: 23764491 INFO @ Mon, 03 Jun 2019 23:00:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:00:59: #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 23:00:59: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:00:59: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:00:59: #1 total tags in treatment: 23764491 INFO @ Mon, 03 Jun 2019 23:00:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:00:59: #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 23:00:59: #1 tags after filtering in treatment: 23764491 INFO @ Mon, 03 Jun 2019 23:00:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:00:59: #1 finished! INFO @ Mon, 03 Jun 2019 23:00:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:00:59: #1 tags after filtering in treatment: 23764491 INFO @ Mon, 03 Jun 2019 23:00:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:00:59: #1 finished! INFO @ Mon, 03 Jun 2019 23:00:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:01:01: #2 number of paired peaks: 116 WARNING @ Mon, 03 Jun 2019 23:01:01: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Mon, 03 Jun 2019 23:01:01: start model_add_line... INFO @ Mon, 03 Jun 2019 23:01:01: start X-correlation... INFO @ Mon, 03 Jun 2019 23:01:01: #2 number of paired peaks: 116 WARNING @ Mon, 03 Jun 2019 23:01:01: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Mon, 03 Jun 2019 23:01:01: start model_add_line... INFO @ Mon, 03 Jun 2019 23:01:01: end of X-cor INFO @ Mon, 03 Jun 2019 23:01:01: #2 finished! INFO @ Mon, 03 Jun 2019 23:01:01: #2 predicted fragment length is 60 bps INFO @ Mon, 03 Jun 2019 23:01:01: #2 alternative fragment length(s) may be 60 bps INFO @ Mon, 03 Jun 2019 23:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.10_model.r WARNING @ Mon, 03 Jun 2019 23:01:01: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:01:01: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Mon, 03 Jun 2019 23:01:01: #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 23:01:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:01:01: start X-correlation... INFO @ Mon, 03 Jun 2019 23:01:01: end of X-cor INFO @ Mon, 03 Jun 2019 23:01:01: #2 finished! INFO @ Mon, 03 Jun 2019 23:01:01: #2 predicted fragment length is 60 bps INFO @ Mon, 03 Jun 2019 23:01:01: #2 alternative fragment length(s) may be 60 bps INFO @ Mon, 03 Jun 2019 23:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.05_model.r WARNING @ Mon, 03 Jun 2019 23:01:01: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:01:01: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Mon, 03 Jun 2019 23:01:01: #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 23:01:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:01:06: 22000000 INFO @ Mon, 03 Jun 2019 23:01:16: 23000000 INFO @ Mon, 03 Jun 2019 23:01:24: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:01:24: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:01:24: #1 total tags in treatment: 23764491 INFO @ Mon, 03 Jun 2019 23:01:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:01:24: #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 23:01:25: #1 tags after filtering in treatment: 23764491 INFO @ Mon, 03 Jun 2019 23:01:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:01:25: #1 finished! INFO @ Mon, 03 Jun 2019 23:01:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:01:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:01:27: #2 number of paired peaks: 116 WARNING @ Mon, 03 Jun 2019 23:01:27: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Mon, 03 Jun 2019 23:01:27: start model_add_line... INFO @ Mon, 03 Jun 2019 23:01:27: start X-correlation... INFO @ Mon, 03 Jun 2019 23:01:27: end of X-cor INFO @ Mon, 03 Jun 2019 23:01:27: #2 finished! INFO @ Mon, 03 Jun 2019 23:01:27: #2 predicted fragment length is 60 bps INFO @ Mon, 03 Jun 2019 23:01:27: #2 alternative fragment length(s) may be 60 bps INFO @ Mon, 03 Jun 2019 23:01:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.20_model.r WARNING @ Mon, 03 Jun 2019 23:01:27: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:01:27: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Mon, 03 Jun 2019 23:01:27: #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 23:01:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:01:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:01:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:01:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:02:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:02:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:02:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:02:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.10_summits.bed INFO @ Mon, 03 Jun 2019 23:02:26: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1421 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:02:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:02:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:02:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.05_summits.bed INFO @ Mon, 03 Jun 2019 23:02:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1935 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:02:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:02:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:02:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343089/SRX5343089.20_summits.bed INFO @ Mon, 03 Jun 2019 23:02:51: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1078 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。