Job ID = 1294537 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:43:18 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 ) 2019-06-02T23:43:37 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 ) 2019-06-02T23:43:37 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 ) 2019-06-02T23:43:37 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 ) 2019-06-02T23:46:26 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 : 20,100,950 reads read : 20,100,950 reads written : 20,100,950 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:32 20100950 reads; of these: 20100950 (100.00%) were unpaired; of these: 1730189 (8.61%) aligned 0 times 14305014 (71.17%) aligned exactly 1 time 4065747 (20.23%) aligned >1 times 91.39% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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] 2335439 / 18370761 = 0.1271 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 09:07:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.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 09:07:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:07:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:07:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.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 09:07:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:07:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:07:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.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 09:07:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:07:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:08:04: 1000000 INFO @ Mon, 03 Jun 2019 09:08:05: 1000000 INFO @ Mon, 03 Jun 2019 09:08:05: 1000000 INFO @ Mon, 03 Jun 2019 09:08:12: 2000000 INFO @ Mon, 03 Jun 2019 09:08:13: 2000000 INFO @ Mon, 03 Jun 2019 09:08:13: 2000000 INFO @ Mon, 03 Jun 2019 09:08:20: 3000000 INFO @ Mon, 03 Jun 2019 09:08:21: 3000000 INFO @ Mon, 03 Jun 2019 09:08:21: 3000000 INFO @ Mon, 03 Jun 2019 09:08:27: 4000000 INFO @ Mon, 03 Jun 2019 09:08:28: 4000000 INFO @ Mon, 03 Jun 2019 09:08:29: 4000000 INFO @ Mon, 03 Jun 2019 09:08:35: 5000000 INFO @ Mon, 03 Jun 2019 09:08:36: 5000000 INFO @ Mon, 03 Jun 2019 09:08:37: 5000000 INFO @ Mon, 03 Jun 2019 09:08:42: 6000000 INFO @ Mon, 03 Jun 2019 09:08:44: 6000000 INFO @ Mon, 03 Jun 2019 09:08:44: 6000000 INFO @ Mon, 03 Jun 2019 09:08:49: 7000000 INFO @ Mon, 03 Jun 2019 09:08:52: 7000000 INFO @ Mon, 03 Jun 2019 09:08:52: 7000000 INFO @ Mon, 03 Jun 2019 09:08:57: 8000000 INFO @ Mon, 03 Jun 2019 09:08:59: 8000000 INFO @ Mon, 03 Jun 2019 09:09:00: 8000000 INFO @ Mon, 03 Jun 2019 09:09:04: 9000000 INFO @ Mon, 03 Jun 2019 09:09:07: 9000000 INFO @ Mon, 03 Jun 2019 09:09:08: 9000000 INFO @ Mon, 03 Jun 2019 09:09:12: 10000000 INFO @ Mon, 03 Jun 2019 09:09:15: 10000000 INFO @ Mon, 03 Jun 2019 09:09:16: 10000000 INFO @ Mon, 03 Jun 2019 09:09:19: 11000000 INFO @ Mon, 03 Jun 2019 09:09:22: 11000000 INFO @ Mon, 03 Jun 2019 09:09:23: 11000000 INFO @ Mon, 03 Jun 2019 09:09:26: 12000000 INFO @ Mon, 03 Jun 2019 09:09:30: 12000000 INFO @ Mon, 03 Jun 2019 09:09:31: 12000000 INFO @ Mon, 03 Jun 2019 09:09:34: 13000000 INFO @ Mon, 03 Jun 2019 09:09:37: 13000000 INFO @ Mon, 03 Jun 2019 09:09:39: 13000000 INFO @ Mon, 03 Jun 2019 09:09:41: 14000000 INFO @ Mon, 03 Jun 2019 09:09:45: 14000000 INFO @ Mon, 03 Jun 2019 09:09:47: 14000000 INFO @ Mon, 03 Jun 2019 09:09:49: 15000000 INFO @ Mon, 03 Jun 2019 09:09:53: 15000000 INFO @ Mon, 03 Jun 2019 09:09:54: 15000000 INFO @ Mon, 03 Jun 2019 09:09:56: 16000000 INFO @ Mon, 03 Jun 2019 09:09:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:09:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:09:57: #1 total tags in treatment: 16035322 INFO @ Mon, 03 Jun 2019 09:09:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:09:57: #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 09:09:57: #1 tags after filtering in treatment: 16035322 INFO @ Mon, 03 Jun 2019 09:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:09:57: #1 finished! INFO @ Mon, 03 Jun 2019 09:09:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:09:58: #2 number of paired peaks: 144 WARNING @ Mon, 03 Jun 2019 09:09:58: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Mon, 03 Jun 2019 09:09:58: start model_add_line... INFO @ Mon, 03 Jun 2019 09:09:58: start X-correlation... INFO @ Mon, 03 Jun 2019 09:09:58: end of X-cor INFO @ Mon, 03 Jun 2019 09:09:58: #2 finished! INFO @ Mon, 03 Jun 2019 09:09:58: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 09:09:58: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 09:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.20_model.r WARNING @ Mon, 03 Jun 2019 09:09:58: #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 09:09:58: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 09:09:58: #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 09:09:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:10:00: 16000000 INFO @ Mon, 03 Jun 2019 09:10:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:10:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:10:01: #1 total tags in treatment: 16035322 INFO @ Mon, 03 Jun 2019 09:10:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:10:01: #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 09:10:01: #1 tags after filtering in treatment: 16035322 INFO @ Mon, 03 Jun 2019 09:10:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:10:01: #1 finished! INFO @ Mon, 03 Jun 2019 09:10:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:10:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:10:02: 16000000 INFO @ Mon, 03 Jun 2019 09:10:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:10:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:10:02: #1 total tags in treatment: 16035322 INFO @ Mon, 03 Jun 2019 09:10:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:10:02: #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 09:10:02: #2 number of paired peaks: 144 WARNING @ Mon, 03 Jun 2019 09:10:02: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Mon, 03 Jun 2019 09:10:02: start model_add_line... INFO @ Mon, 03 Jun 2019 09:10:03: start X-correlation... INFO @ Mon, 03 Jun 2019 09:10:03: end of X-cor INFO @ Mon, 03 Jun 2019 09:10:03: #2 finished! INFO @ Mon, 03 Jun 2019 09:10:03: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 09:10:03: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 09:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.10_model.r WARNING @ Mon, 03 Jun 2019 09:10:03: #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 09:10:03: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 09:10:03: #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 09:10:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:10:03: #1 tags after filtering in treatment: 16035322 INFO @ Mon, 03 Jun 2019 09:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:10:03: #1 finished! INFO @ Mon, 03 Jun 2019 09:10:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:10:04: #2 number of paired peaks: 144 WARNING @ Mon, 03 Jun 2019 09:10:04: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Mon, 03 Jun 2019 09:10:04: start model_add_line... INFO @ Mon, 03 Jun 2019 09:10:04: start X-correlation... INFO @ Mon, 03 Jun 2019 09:10:04: end of X-cor INFO @ Mon, 03 Jun 2019 09:10:04: #2 finished! INFO @ Mon, 03 Jun 2019 09:10:04: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 09:10:04: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 09:10:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.05_model.r WARNING @ Mon, 03 Jun 2019 09:10:04: #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 09:10:04: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 09:10:04: #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 09:10:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:10:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:10:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:10:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:11:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:11:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:11:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.20_summits.bed INFO @ Mon, 03 Jun 2019 09:11:02: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (639 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:11:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:11:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.10_summits.bed INFO @ Mon, 03 Jun 2019 09:11:07: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1339 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:11:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:11:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:11:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287726/SRX287726.05_summits.bed INFO @ Mon, 03 Jun 2019 09:11:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1805 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。