Job ID = 1294527 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:43:25 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 ) 2019-06-02T23:43:25 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 ) 2019-06-02T23:43:25 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 ) 2019-06-02T23:45:53 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 ) 2019-06-02T23:50:50 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 ) 2019-06-02T23:54:37 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 : 19,415,913 reads read : 19,415,913 reads written : 19,415,913 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: 00:11:10 19415913 reads; of these: 19415913 (100.00%) were unpaired; of these: 1262032 (6.50%) aligned 0 times 8305945 (42.78%) aligned exactly 1 time 9847936 (50.72%) aligned >1 times 93.50% overall alignment rate Time searching: 00:11:10 Overall time: 00:11:10 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] 3177036 / 18153881 = 0.1750 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 09:12:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.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 09:12:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:12:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:12:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.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 09:12:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:12:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:12:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.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 09:12:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:12:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:12:20: 1000000 INFO @ Mon, 03 Jun 2019 09:12:21: 1000000 INFO @ Mon, 03 Jun 2019 09:12:21: 1000000 INFO @ Mon, 03 Jun 2019 09:12:27: 2000000 INFO @ Mon, 03 Jun 2019 09:12:29: 2000000 INFO @ Mon, 03 Jun 2019 09:12:29: 2000000 INFO @ Mon, 03 Jun 2019 09:12:34: 3000000 INFO @ Mon, 03 Jun 2019 09:12:37: 3000000 INFO @ Mon, 03 Jun 2019 09:12:37: 3000000 INFO @ Mon, 03 Jun 2019 09:12:41: 4000000 INFO @ Mon, 03 Jun 2019 09:12:45: 4000000 INFO @ Mon, 03 Jun 2019 09:12:45: 4000000 INFO @ Mon, 03 Jun 2019 09:12:49: 5000000 INFO @ Mon, 03 Jun 2019 09:12:53: 5000000 INFO @ Mon, 03 Jun 2019 09:12:54: 5000000 INFO @ Mon, 03 Jun 2019 09:12:56: 6000000 INFO @ Mon, 03 Jun 2019 09:13:00: 6000000 INFO @ Mon, 03 Jun 2019 09:13:03: 6000000 INFO @ Mon, 03 Jun 2019 09:13:03: 7000000 INFO @ Mon, 03 Jun 2019 09:13:08: 7000000 INFO @ Mon, 03 Jun 2019 09:13:10: 8000000 INFO @ Mon, 03 Jun 2019 09:13:11: 7000000 INFO @ Mon, 03 Jun 2019 09:13:16: 8000000 INFO @ Mon, 03 Jun 2019 09:13:17: 9000000 INFO @ Mon, 03 Jun 2019 09:13:19: 8000000 INFO @ Mon, 03 Jun 2019 09:13:24: 9000000 INFO @ Mon, 03 Jun 2019 09:13:24: 10000000 INFO @ Mon, 03 Jun 2019 09:13:27: 9000000 INFO @ Mon, 03 Jun 2019 09:13:32: 10000000 INFO @ Mon, 03 Jun 2019 09:13:33: 11000000 INFO @ Mon, 03 Jun 2019 09:13:35: 10000000 INFO @ Mon, 03 Jun 2019 09:13:40: 11000000 INFO @ Mon, 03 Jun 2019 09:13:40: 12000000 INFO @ Mon, 03 Jun 2019 09:13:43: 11000000 INFO @ Mon, 03 Jun 2019 09:13:47: 13000000 INFO @ Mon, 03 Jun 2019 09:13:47: 12000000 INFO @ Mon, 03 Jun 2019 09:13:51: 12000000 INFO @ Mon, 03 Jun 2019 09:13:54: 14000000 INFO @ Mon, 03 Jun 2019 09:13:55: 13000000 INFO @ Mon, 03 Jun 2019 09:13:59: 13000000 INFO @ Mon, 03 Jun 2019 09:14:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:14:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:14:02: #1 total tags in treatment: 14976845 INFO @ Mon, 03 Jun 2019 09:14:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:14:02: #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 09:14:02: #1 tags after filtering in treatment: 14976845 INFO @ Mon, 03 Jun 2019 09:14:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:14:02: #1 finished! INFO @ Mon, 03 Jun 2019 09:14:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:14:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:14:02: 14000000 INFO @ Mon, 03 Jun 2019 09:14:03: #2 number of paired peaks: 760 WARNING @ Mon, 03 Jun 2019 09:14:03: Fewer paired peaks (760) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 760 pairs to build model! INFO @ Mon, 03 Jun 2019 09:14:03: start model_add_line... INFO @ Mon, 03 Jun 2019 09:14:03: start X-correlation... INFO @ Mon, 03 Jun 2019 09:14:03: end of X-cor INFO @ Mon, 03 Jun 2019 09:14:03: #2 finished! INFO @ Mon, 03 Jun 2019 09:14:03: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:14:03: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:14:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.10_model.r WARNING @ Mon, 03 Jun 2019 09:14:03: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:14:03: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:14:03: #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 09:14:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:14:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:14:07: 14000000 INFO @ Mon, 03 Jun 2019 09:14:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:14:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:14:10: #1 total tags in treatment: 14976845 INFO @ Mon, 03 Jun 2019 09:14:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:14:10: #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 09:14:10: #1 tags after filtering in treatment: 14976845 INFO @ Mon, 03 Jun 2019 09:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:14:10: #1 finished! INFO @ Mon, 03 Jun 2019 09:14:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:14:12: #2 number of paired peaks: 760 WARNING @ Mon, 03 Jun 2019 09:14:12: Fewer paired peaks (760) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 760 pairs to build model! INFO @ Mon, 03 Jun 2019 09:14:12: start model_add_line... INFO @ Mon, 03 Jun 2019 09:14:12: start X-correlation... INFO @ Mon, 03 Jun 2019 09:14:12: end of X-cor INFO @ Mon, 03 Jun 2019 09:14:12: #2 finished! INFO @ Mon, 03 Jun 2019 09:14:12: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:14:12: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:14:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.20_model.r WARNING @ Mon, 03 Jun 2019 09:14:12: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:14:12: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:14:12: #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 09:14:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:14:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:14:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:14:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:14:14: #1 total tags in treatment: 14976845 INFO @ Mon, 03 Jun 2019 09:14:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:14:14: #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 09:14:14: #1 tags after filtering in treatment: 14976845 INFO @ Mon, 03 Jun 2019 09:14:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:14:14: #1 finished! INFO @ Mon, 03 Jun 2019 09:14:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:14:16: #2 number of paired peaks: 760 WARNING @ Mon, 03 Jun 2019 09:14:16: Fewer paired peaks (760) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 760 pairs to build model! INFO @ Mon, 03 Jun 2019 09:14:16: start model_add_line... INFO @ Mon, 03 Jun 2019 09:14:16: start X-correlation... INFO @ Mon, 03 Jun 2019 09:14:16: end of X-cor INFO @ Mon, 03 Jun 2019 09:14:16: #2 finished! INFO @ Mon, 03 Jun 2019 09:14:16: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:14:16: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:14:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.05_model.r WARNING @ Mon, 03 Jun 2019 09:14:16: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:14:16: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:14:16: #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 09:14:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:14:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:14:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:14:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:14:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:15:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:15:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:15:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.10_summits.bed INFO @ Mon, 03 Jun 2019 09:15:03: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1967 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:15:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:15:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:15:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.20_summits.bed INFO @ Mon, 03 Jun 2019 09:15:10: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1201 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:15:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:15:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287720/SRX287720.05_summits.bed INFO @ Mon, 03 Jun 2019 09:15:16: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3732 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。