Job ID = 1300023 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T09:42:54 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 ) 2019-06-03T09:42:54 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 ) 2019-06-03T09:42:54 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 ) 2019-06-03T09:43:23 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T09:46:24 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 ) spots read : 15,442,783 reads read : 15,442,783 reads written : 15,442,783 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: 00:07:28 15442783 reads; of these: 15442783 (100.00%) were unpaired; of these: 559002 (3.62%) aligned 0 times 10185378 (65.96%) aligned exactly 1 time 4698403 (30.42%) aligned >1 times 96.38% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 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] 1521800 / 14883781 = 0.1022 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 19:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.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 19:06:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:06:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.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 19:06:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:06:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.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 19:06:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:06:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:06:29: 1000000 INFO @ Mon, 03 Jun 2019 19:06:29: 1000000 INFO @ Mon, 03 Jun 2019 19:06:31: 1000000 INFO @ Mon, 03 Jun 2019 19:06:37: 2000000 INFO @ Mon, 03 Jun 2019 19:06:37: 2000000 INFO @ Mon, 03 Jun 2019 19:06:41: 2000000 INFO @ Mon, 03 Jun 2019 19:06:45: 3000000 INFO @ Mon, 03 Jun 2019 19:06:45: 3000000 INFO @ Mon, 03 Jun 2019 19:06:51: 3000000 INFO @ Mon, 03 Jun 2019 19:06:54: 4000000 INFO @ Mon, 03 Jun 2019 19:06:54: 4000000 INFO @ Mon, 03 Jun 2019 19:07:01: 4000000 INFO @ Mon, 03 Jun 2019 19:07:02: 5000000 INFO @ Mon, 03 Jun 2019 19:07:02: 5000000 INFO @ Mon, 03 Jun 2019 19:07:10: 6000000 INFO @ Mon, 03 Jun 2019 19:07:10: 6000000 INFO @ Mon, 03 Jun 2019 19:07:11: 5000000 INFO @ Mon, 03 Jun 2019 19:07:19: 7000000 INFO @ Mon, 03 Jun 2019 19:07:19: 7000000 INFO @ Mon, 03 Jun 2019 19:07:21: 6000000 INFO @ Mon, 03 Jun 2019 19:07:27: 8000000 INFO @ Mon, 03 Jun 2019 19:07:27: 8000000 INFO @ Mon, 03 Jun 2019 19:07:30: 7000000 INFO @ Mon, 03 Jun 2019 19:07:35: 9000000 INFO @ Mon, 03 Jun 2019 19:07:35: 9000000 INFO @ Mon, 03 Jun 2019 19:07:40: 8000000 INFO @ Mon, 03 Jun 2019 19:07:44: 10000000 INFO @ Mon, 03 Jun 2019 19:07:44: 10000000 INFO @ Mon, 03 Jun 2019 19:07:50: 9000000 INFO @ Mon, 03 Jun 2019 19:07:52: 11000000 INFO @ Mon, 03 Jun 2019 19:07:52: 11000000 INFO @ Mon, 03 Jun 2019 19:08:00: 10000000 INFO @ Mon, 03 Jun 2019 19:08:00: 12000000 INFO @ Mon, 03 Jun 2019 19:08:00: 12000000 INFO @ Mon, 03 Jun 2019 19:08:08: 13000000 INFO @ Mon, 03 Jun 2019 19:08:08: 13000000 INFO @ Mon, 03 Jun 2019 19:08:10: 11000000 INFO @ Mon, 03 Jun 2019 19:08:12: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:08:12: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:08:12: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:08:12: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:08:12: #1 total tags in treatment: 13361981 INFO @ Mon, 03 Jun 2019 19:08:12: #1 total tags in treatment: 13361981 INFO @ Mon, 03 Jun 2019 19:08:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:08:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:08:12: #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 19:08:12: #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 19:08:12: #1 tags after filtering in treatment: 13361981 INFO @ Mon, 03 Jun 2019 19:08:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:08:12: #1 finished! INFO @ Mon, 03 Jun 2019 19:08:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:08:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:08:12: #1 tags after filtering in treatment: 13361981 INFO @ Mon, 03 Jun 2019 19:08:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:08:12: #1 finished! INFO @ Mon, 03 Jun 2019 19:08:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:08:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:08:13: #2 number of paired peaks: 958 WARNING @ Mon, 03 Jun 2019 19:08:13: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Mon, 03 Jun 2019 19:08:13: start model_add_line... INFO @ Mon, 03 Jun 2019 19:08:13: #2 number of paired peaks: 958 WARNING @ Mon, 03 Jun 2019 19:08:13: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Mon, 03 Jun 2019 19:08:13: start model_add_line... INFO @ Mon, 03 Jun 2019 19:08:13: start X-correlation... INFO @ Mon, 03 Jun 2019 19:08:13: start X-correlation... INFO @ Mon, 03 Jun 2019 19:08:13: end of X-cor INFO @ Mon, 03 Jun 2019 19:08:13: end of X-cor INFO @ Mon, 03 Jun 2019 19:08:13: #2 finished! INFO @ Mon, 03 Jun 2019 19:08:13: #2 finished! INFO @ Mon, 03 Jun 2019 19:08:13: #2 predicted fragment length is 67 bps INFO @ Mon, 03 Jun 2019 19:08:13: #2 predicted fragment length is 67 bps INFO @ Mon, 03 Jun 2019 19:08:13: #2 alternative fragment length(s) may be 3,67 bps INFO @ Mon, 03 Jun 2019 19:08:13: #2 alternative fragment length(s) may be 3,67 bps INFO @ Mon, 03 Jun 2019 19:08:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.20_model.r INFO @ Mon, 03 Jun 2019 19:08:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.10_model.r WARNING @ Mon, 03 Jun 2019 19:08:13: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:08:13: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:08:13: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Mon, 03 Jun 2019 19:08:13: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Mon, 03 Jun 2019 19:08:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Mon, 03 Jun 2019 19:08:13: #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 19:08:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:08:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:08:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:08:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:08:20: 12000000 INFO @ Mon, 03 Jun 2019 19:08:29: 13000000 INFO @ Mon, 03 Jun 2019 19:08:33: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:08:33: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:08:33: #1 total tags in treatment: 13361981 INFO @ Mon, 03 Jun 2019 19:08:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:08:33: #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 19:08:33: #1 tags after filtering in treatment: 13361981 INFO @ Mon, 03 Jun 2019 19:08:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:08:33: #1 finished! INFO @ Mon, 03 Jun 2019 19:08:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:08:35: #2 number of paired peaks: 958 WARNING @ Mon, 03 Jun 2019 19:08:35: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Mon, 03 Jun 2019 19:08:35: start model_add_line... INFO @ Mon, 03 Jun 2019 19:08:35: start X-correlation... INFO @ Mon, 03 Jun 2019 19:08:35: end of X-cor INFO @ Mon, 03 Jun 2019 19:08:35: #2 finished! INFO @ Mon, 03 Jun 2019 19:08:35: #2 predicted fragment length is 67 bps INFO @ Mon, 03 Jun 2019 19:08:35: #2 alternative fragment length(s) may be 3,67 bps INFO @ Mon, 03 Jun 2019 19:08:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.05_model.r WARNING @ Mon, 03 Jun 2019 19:08:35: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:08:35: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Mon, 03 Jun 2019 19:08:35: #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 19:08:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:08:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:08:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:08:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:09:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:09:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:09:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:09:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:09:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.20_summits.bed INFO @ Mon, 03 Jun 2019 19:09:08: Done! INFO @ Mon, 03 Jun 2019 19:09:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.10_summits.bed INFO @ Mon, 03 Jun 2019 19:09:08: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (880 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1860 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:09:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:09:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:09:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:09:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801802/SRX4801802.05_summits.bed INFO @ Mon, 03 Jun 2019 19:09:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3326 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。