Job ID = 1294823 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:17:56 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 ) 2019-06-03T01:17:56 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 ) 2019-06-03T01:17:56 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 ) 2019-06-03T01:20:24 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 ) 2019-06-03T01:23:28 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 : 16,856,264 reads read : 16,856,264 reads written : 16,856,264 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: 00:06:54 16856264 reads; of these: 16856264 (100.00%) were unpaired; of these: 886527 (5.26%) aligned 0 times 11886710 (70.52%) aligned exactly 1 time 4083027 (24.22%) aligned >1 times 94.74% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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] 1506003 / 15969737 = 0.0943 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 10:37:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.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 10:37:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:37:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:37:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.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 10:37:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.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 10:37:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:37:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:37:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:37:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:37:50: 1000000 INFO @ Mon, 03 Jun 2019 10:37:51: 1000000 INFO @ Mon, 03 Jun 2019 10:37:52: 1000000 INFO @ Mon, 03 Jun 2019 10:37:57: 2000000 INFO @ Mon, 03 Jun 2019 10:37:59: 2000000 INFO @ Mon, 03 Jun 2019 10:37:59: 2000000 INFO @ Mon, 03 Jun 2019 10:38:05: 3000000 INFO @ Mon, 03 Jun 2019 10:38:08: 3000000 INFO @ Mon, 03 Jun 2019 10:38:08: 3000000 INFO @ Mon, 03 Jun 2019 10:38:13: 4000000 INFO @ Mon, 03 Jun 2019 10:38:16: 4000000 INFO @ Mon, 03 Jun 2019 10:38:16: 4000000 INFO @ Mon, 03 Jun 2019 10:38:21: 5000000 INFO @ Mon, 03 Jun 2019 10:38:24: 5000000 INFO @ Mon, 03 Jun 2019 10:38:25: 5000000 INFO @ Mon, 03 Jun 2019 10:38:30: 6000000 INFO @ Mon, 03 Jun 2019 10:38:33: 6000000 INFO @ Mon, 03 Jun 2019 10:38:33: 6000000 INFO @ Mon, 03 Jun 2019 10:38:38: 7000000 INFO @ Mon, 03 Jun 2019 10:38:42: 7000000 INFO @ Mon, 03 Jun 2019 10:38:42: 7000000 INFO @ Mon, 03 Jun 2019 10:38:47: 8000000 INFO @ Mon, 03 Jun 2019 10:38:50: 8000000 INFO @ Mon, 03 Jun 2019 10:38:51: 8000000 INFO @ Mon, 03 Jun 2019 10:38:56: 9000000 INFO @ Mon, 03 Jun 2019 10:38:59: 9000000 INFO @ Mon, 03 Jun 2019 10:38:59: 9000000 INFO @ Mon, 03 Jun 2019 10:39:03: 10000000 INFO @ Mon, 03 Jun 2019 10:39:07: 10000000 INFO @ Mon, 03 Jun 2019 10:39:08: 10000000 INFO @ Mon, 03 Jun 2019 10:39:11: 11000000 INFO @ Mon, 03 Jun 2019 10:39:15: 11000000 INFO @ Mon, 03 Jun 2019 10:39:16: 11000000 INFO @ Mon, 03 Jun 2019 10:39:20: 12000000 INFO @ Mon, 03 Jun 2019 10:39:23: 12000000 INFO @ Mon, 03 Jun 2019 10:39:24: 12000000 INFO @ Mon, 03 Jun 2019 10:39:27: 13000000 INFO @ Mon, 03 Jun 2019 10:39:31: 13000000 INFO @ Mon, 03 Jun 2019 10:39:32: 13000000 INFO @ Mon, 03 Jun 2019 10:39:35: 14000000 INFO @ Mon, 03 Jun 2019 10:39:39: 14000000 INFO @ Mon, 03 Jun 2019 10:39:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:39:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:39:39: #1 total tags in treatment: 14463734 INFO @ Mon, 03 Jun 2019 10:39:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:39:39: #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 10:39:40: #1 tags after filtering in treatment: 14463734 INFO @ Mon, 03 Jun 2019 10:39:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:39:40: #1 finished! INFO @ Mon, 03 Jun 2019 10:39:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:39:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:39:40: 14000000 INFO @ Mon, 03 Jun 2019 10:39:41: #2 number of paired peaks: 120 WARNING @ Mon, 03 Jun 2019 10:39:41: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 03 Jun 2019 10:39:41: start model_add_line... INFO @ Mon, 03 Jun 2019 10:39:41: start X-correlation... INFO @ Mon, 03 Jun 2019 10:39:41: end of X-cor INFO @ Mon, 03 Jun 2019 10:39:41: #2 finished! INFO @ Mon, 03 Jun 2019 10:39:41: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 10:39:41: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 10:39:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.10_model.r WARNING @ Mon, 03 Jun 2019 10:39:41: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:39:41: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 10:39:41: #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 10:39:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:39:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:39:42: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:39:42: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:39:42: #1 total tags in treatment: 14463734 INFO @ Mon, 03 Jun 2019 10:39:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:39:42: #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 10:39:42: #1 tags after filtering in treatment: 14463734 INFO @ Mon, 03 Jun 2019 10:39:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:39:42: #1 finished! INFO @ Mon, 03 Jun 2019 10:39:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:39:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:39:44: #2 number of paired peaks: 120 WARNING @ Mon, 03 Jun 2019 10:39:44: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 03 Jun 2019 10:39:44: start model_add_line... INFO @ Mon, 03 Jun 2019 10:39:44: start X-correlation... INFO @ Mon, 03 Jun 2019 10:39:44: end of X-cor INFO @ Mon, 03 Jun 2019 10:39:44: #2 finished! INFO @ Mon, 03 Jun 2019 10:39:44: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 10:39:44: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 10:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.20_model.r WARNING @ Mon, 03 Jun 2019 10:39:44: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:39:44: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 10:39:44: #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 10:39:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:39:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:39:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:39:44: #1 total tags in treatment: 14463734 INFO @ Mon, 03 Jun 2019 10:39:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:39:44: #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 10:39:44: #1 tags after filtering in treatment: 14463734 INFO @ Mon, 03 Jun 2019 10:39:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:39:44: #1 finished! INFO @ Mon, 03 Jun 2019 10:39:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:39:45: #2 number of paired peaks: 120 WARNING @ Mon, 03 Jun 2019 10:39:45: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 03 Jun 2019 10:39:45: start model_add_line... INFO @ Mon, 03 Jun 2019 10:39:46: start X-correlation... INFO @ Mon, 03 Jun 2019 10:39:46: end of X-cor INFO @ Mon, 03 Jun 2019 10:39:46: #2 finished! INFO @ Mon, 03 Jun 2019 10:39:46: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 10:39:46: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 10:39:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.05_model.r WARNING @ Mon, 03 Jun 2019 10:39:46: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:39:46: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 10:39:46: #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 10:39:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:39:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:40:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:40:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:40:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:40:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:40:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:40:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.10_summits.bed INFO @ Mon, 03 Jun 2019 10:40:38: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1666 records, 4 fields): 62 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:40:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:40:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:40:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.20_summits.bed INFO @ Mon, 03 Jun 2019 10:40:41: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1155 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:40:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:40:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:40:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287922/SRX287922.05_summits.bed INFO @ Mon, 03 Jun 2019 10:40:44: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1956 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。