Job ID = 1294701 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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 ) 2019-06-03T00:41:44 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 ) 2019-06-03T00:41:44 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 ) 2019-06-03T00:41:44 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 ) 2019-06-03T00:41:44 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 ) 2019-06-03T00:48:00 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 : 17,133,552 reads read : 17,133,552 reads written : 17,133,552 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: 00:08:08 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 669303 (3.91%) aligned 0 times 11145593 (65.05%) aligned exactly 1 time 5318656 (31.04%) aligned >1 times 96.09% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 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] 2378848 / 16464249 = 0.1445 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 10:02:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.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 10:02:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:02:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:02:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.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 10:02:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:02:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:02:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.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 10:02:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:02:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:02:25: 1000000 INFO @ Mon, 03 Jun 2019 10:02:27: 1000000 INFO @ Mon, 03 Jun 2019 10:02:27: 1000000 INFO @ Mon, 03 Jun 2019 10:02:33: 2000000 INFO @ Mon, 03 Jun 2019 10:02:37: 2000000 INFO @ Mon, 03 Jun 2019 10:02:37: 2000000 INFO @ Mon, 03 Jun 2019 10:02:41: 3000000 INFO @ Mon, 03 Jun 2019 10:02:46: 3000000 INFO @ Mon, 03 Jun 2019 10:02:46: 3000000 INFO @ Mon, 03 Jun 2019 10:02:50: 4000000 INFO @ Mon, 03 Jun 2019 10:02:56: 4000000 INFO @ Mon, 03 Jun 2019 10:02:56: 4000000 INFO @ Mon, 03 Jun 2019 10:02:58: 5000000 INFO @ Mon, 03 Jun 2019 10:03:06: 5000000 INFO @ Mon, 03 Jun 2019 10:03:06: 6000000 INFO @ Mon, 03 Jun 2019 10:03:06: 5000000 INFO @ Mon, 03 Jun 2019 10:03:14: 7000000 INFO @ Mon, 03 Jun 2019 10:03:15: 6000000 INFO @ Mon, 03 Jun 2019 10:03:15: 6000000 INFO @ Mon, 03 Jun 2019 10:03:22: 8000000 INFO @ Mon, 03 Jun 2019 10:03:25: 7000000 INFO @ Mon, 03 Jun 2019 10:03:25: 7000000 INFO @ Mon, 03 Jun 2019 10:03:30: 9000000 INFO @ Mon, 03 Jun 2019 10:03:34: 8000000 INFO @ Mon, 03 Jun 2019 10:03:34: 8000000 INFO @ Mon, 03 Jun 2019 10:03:38: 10000000 INFO @ Mon, 03 Jun 2019 10:03:44: 9000000 INFO @ Mon, 03 Jun 2019 10:03:44: 9000000 INFO @ Mon, 03 Jun 2019 10:03:46: 11000000 INFO @ Mon, 03 Jun 2019 10:03:54: 12000000 INFO @ Mon, 03 Jun 2019 10:03:54: 10000000 INFO @ Mon, 03 Jun 2019 10:03:54: 10000000 INFO @ Mon, 03 Jun 2019 10:04:01: 13000000 INFO @ Mon, 03 Jun 2019 10:04:03: 11000000 INFO @ Mon, 03 Jun 2019 10:04:03: 11000000 INFO @ Mon, 03 Jun 2019 10:04:09: 14000000 INFO @ Mon, 03 Jun 2019 10:04:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:04:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:04:10: #1 total tags in treatment: 14085401 INFO @ Mon, 03 Jun 2019 10:04:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:04:10: #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 10:04:10: #1 tags after filtering in treatment: 14085401 INFO @ Mon, 03 Jun 2019 10:04:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:04:10: #1 finished! INFO @ Mon, 03 Jun 2019 10:04:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:04:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:04:12: #2 number of paired peaks: 359 WARNING @ Mon, 03 Jun 2019 10:04:12: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Mon, 03 Jun 2019 10:04:12: start model_add_line... INFO @ Mon, 03 Jun 2019 10:04:12: start X-correlation... INFO @ Mon, 03 Jun 2019 10:04:12: end of X-cor INFO @ Mon, 03 Jun 2019 10:04:12: #2 finished! INFO @ Mon, 03 Jun 2019 10:04:12: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 10:04:12: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 10:04:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.20_model.r WARNING @ Mon, 03 Jun 2019 10:04:12: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:04:12: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 10:04:12: #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 10:04:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:04:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:04:13: 12000000 INFO @ Mon, 03 Jun 2019 10:04:13: 12000000 INFO @ Mon, 03 Jun 2019 10:04:22: 13000000 INFO @ Mon, 03 Jun 2019 10:04:22: 13000000 INFO @ Mon, 03 Jun 2019 10:04:32: 14000000 INFO @ Mon, 03 Jun 2019 10:04:32: 14000000 INFO @ Mon, 03 Jun 2019 10:04:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:04:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:04:33: #1 total tags in treatment: 14085401 INFO @ Mon, 03 Jun 2019 10:04:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:04:33: #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 10:04:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:04:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:04:33: #1 total tags in treatment: 14085401 INFO @ Mon, 03 Jun 2019 10:04:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:04:33: #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 10:04:33: #1 tags after filtering in treatment: 14085401 INFO @ Mon, 03 Jun 2019 10:04:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:04:33: #1 finished! INFO @ Mon, 03 Jun 2019 10:04:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:04:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:04:33: #1 tags after filtering in treatment: 14085401 INFO @ Mon, 03 Jun 2019 10:04:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:04:33: #1 finished! INFO @ Mon, 03 Jun 2019 10:04:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:04:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:04:34: #2 number of paired peaks: 359 WARNING @ Mon, 03 Jun 2019 10:04:34: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Mon, 03 Jun 2019 10:04:34: start model_add_line... INFO @ Mon, 03 Jun 2019 10:04:34: start X-correlation... INFO @ Mon, 03 Jun 2019 10:04:34: end of X-cor INFO @ Mon, 03 Jun 2019 10:04:34: #2 finished! INFO @ Mon, 03 Jun 2019 10:04:34: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 10:04:34: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 10:04:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.10_model.r WARNING @ Mon, 03 Jun 2019 10:04:34: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:04:34: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 10:04:34: #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 10:04:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:04:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:04:34: #2 number of paired peaks: 359 WARNING @ Mon, 03 Jun 2019 10:04:34: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Mon, 03 Jun 2019 10:04:34: start model_add_line... INFO @ Mon, 03 Jun 2019 10:04:34: start X-correlation... INFO @ Mon, 03 Jun 2019 10:04:34: end of X-cor INFO @ Mon, 03 Jun 2019 10:04:34: #2 finished! INFO @ Mon, 03 Jun 2019 10:04:34: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 10:04:34: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 10:04:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.05_model.r WARNING @ Mon, 03 Jun 2019 10:04:34: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:04:34: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 10:04:34: #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 10:04:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:04:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:04:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:05:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:05:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:05:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.20_summits.bed INFO @ Mon, 03 Jun 2019 10:05:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1483 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:05:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:05:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:05:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:05:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:05:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.10_summits.bed INFO @ Mon, 03 Jun 2019 10:05:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:05:31: Done! INFO @ Mon, 03 Jun 2019 10:05:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:05:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287830/SRX287830.05_summits.bed INFO @ Mon, 03 Jun 2019 10:05:31: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1929 records, 4 fields): 9 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2214 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。