Job ID = 1293675 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:31:06 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 ) 2019-06-02T16:31:06 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 ) 2019-06-02T16:32:30 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 ) 2019-06-02T16:38:25 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 ) 2019-06-02T16:38:25 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 ) spots read : 17,724,933 reads read : 17,724,933 reads written : 17,724,933 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: 00:09:09 17724933 reads; of these: 17724933 (100.00%) were unpaired; of these: 1854901 (10.46%) aligned 0 times 11508184 (64.93%) aligned exactly 1 time 4361848 (24.61%) aligned >1 times 89.54% overall alignment rate Time searching: 00:09:09 Overall time: 00:09:09 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] 1986808 / 15870032 = 0.1252 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 01:55:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.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 01:55:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:55:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:55:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.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 01:55:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:55:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:55:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.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 01:55:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:55:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:55:21: 1000000 INFO @ Mon, 03 Jun 2019 01:55:22: 1000000 INFO @ Mon, 03 Jun 2019 01:55:23: 1000000 INFO @ Mon, 03 Jun 2019 01:55:31: 2000000 INFO @ Mon, 03 Jun 2019 01:55:33: 2000000 INFO @ Mon, 03 Jun 2019 01:55:34: 2000000 INFO @ Mon, 03 Jun 2019 01:55:41: 3000000 INFO @ Mon, 03 Jun 2019 01:55:44: 3000000 INFO @ Mon, 03 Jun 2019 01:55:46: 3000000 INFO @ Mon, 03 Jun 2019 01:55:50: 4000000 INFO @ Mon, 03 Jun 2019 01:55:54: 4000000 INFO @ Mon, 03 Jun 2019 01:55:58: 4000000 INFO @ Mon, 03 Jun 2019 01:56:00: 5000000 INFO @ Mon, 03 Jun 2019 01:56:05: 5000000 INFO @ Mon, 03 Jun 2019 01:56:09: 5000000 INFO @ Mon, 03 Jun 2019 01:56:10: 6000000 INFO @ Mon, 03 Jun 2019 01:56:15: 6000000 INFO @ Mon, 03 Jun 2019 01:56:19: 7000000 INFO @ Mon, 03 Jun 2019 01:56:21: 6000000 INFO @ Mon, 03 Jun 2019 01:56:26: 7000000 INFO @ Mon, 03 Jun 2019 01:56:29: 8000000 INFO @ Mon, 03 Jun 2019 01:56:33: 7000000 INFO @ Mon, 03 Jun 2019 01:56:36: 8000000 INFO @ Mon, 03 Jun 2019 01:56:38: 9000000 INFO @ Mon, 03 Jun 2019 01:56:45: 8000000 INFO @ Mon, 03 Jun 2019 01:56:47: 9000000 INFO @ Mon, 03 Jun 2019 01:56:47: 10000000 INFO @ Mon, 03 Jun 2019 01:56:56: 9000000 INFO @ Mon, 03 Jun 2019 01:56:57: 11000000 INFO @ Mon, 03 Jun 2019 01:56:57: 10000000 INFO @ Mon, 03 Jun 2019 01:57:06: 12000000 INFO @ Mon, 03 Jun 2019 01:57:07: 11000000 INFO @ Mon, 03 Jun 2019 01:57:07: 10000000 INFO @ Mon, 03 Jun 2019 01:57:14: 13000000 INFO @ Mon, 03 Jun 2019 01:57:17: 12000000 INFO @ Mon, 03 Jun 2019 01:57:19: 11000000 INFO @ Mon, 03 Jun 2019 01:57:23: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:57:23: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:57:23: #1 total tags in treatment: 13883224 INFO @ Mon, 03 Jun 2019 01:57:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:57:23: #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 01:57:23: #1 tags after filtering in treatment: 13883224 INFO @ Mon, 03 Jun 2019 01:57:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:57:23: #1 finished! INFO @ Mon, 03 Jun 2019 01:57:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:57:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:57:25: #2 number of paired peaks: 275 WARNING @ Mon, 03 Jun 2019 01:57:25: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Mon, 03 Jun 2019 01:57:25: start model_add_line... INFO @ Mon, 03 Jun 2019 01:57:25: start X-correlation... INFO @ Mon, 03 Jun 2019 01:57:25: end of X-cor INFO @ Mon, 03 Jun 2019 01:57:25: #2 finished! INFO @ Mon, 03 Jun 2019 01:57:25: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 01:57:25: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 01:57:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.10_model.r WARNING @ Mon, 03 Jun 2019 01:57:25: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:57:25: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 01:57:25: #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 01:57:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:57:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:57:28: 13000000 INFO @ Mon, 03 Jun 2019 01:57:30: 12000000 INFO @ Mon, 03 Jun 2019 01:57:37: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:57:37: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:57:37: #1 total tags in treatment: 13883224 INFO @ Mon, 03 Jun 2019 01:57:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:57:37: #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 01:57:37: #1 tags after filtering in treatment: 13883224 INFO @ Mon, 03 Jun 2019 01:57:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:57:37: #1 finished! INFO @ Mon, 03 Jun 2019 01:57:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:57:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:57:39: #2 number of paired peaks: 275 WARNING @ Mon, 03 Jun 2019 01:57:39: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Mon, 03 Jun 2019 01:57:39: start model_add_line... INFO @ Mon, 03 Jun 2019 01:57:39: start X-correlation... INFO @ Mon, 03 Jun 2019 01:57:39: end of X-cor INFO @ Mon, 03 Jun 2019 01:57:39: #2 finished! INFO @ Mon, 03 Jun 2019 01:57:39: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 01:57:39: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 01:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.05_model.r WARNING @ Mon, 03 Jun 2019 01:57:39: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:57:39: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 01:57:39: #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 01:57:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:57:39: 13000000 INFO @ Mon, 03 Jun 2019 01:57:48: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:57:48: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:57:48: #1 total tags in treatment: 13883224 INFO @ Mon, 03 Jun 2019 01:57:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:57:48: #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 01:57:48: #1 tags after filtering in treatment: 13883224 INFO @ Mon, 03 Jun 2019 01:57:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:57:48: #1 finished! INFO @ Mon, 03 Jun 2019 01:57:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:57:49: #2 number of paired peaks: 275 WARNING @ Mon, 03 Jun 2019 01:57:49: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Mon, 03 Jun 2019 01:57:49: start model_add_line... INFO @ Mon, 03 Jun 2019 01:57:49: start X-correlation... INFO @ Mon, 03 Jun 2019 01:57:49: end of X-cor INFO @ Mon, 03 Jun 2019 01:57:49: #2 finished! INFO @ Mon, 03 Jun 2019 01:57:49: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 01:57:49: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 01:57:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.20_model.r WARNING @ Mon, 03 Jun 2019 01:57:49: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:57:49: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 01:57:49: #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 01:57:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:57:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:58:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:58:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:58:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:58:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:58:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.10_summits.bed INFO @ Mon, 03 Jun 2019 01:58:25: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1369 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:58:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:58:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:58:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:58:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.05_summits.bed INFO @ Mon, 03 Jun 2019 01:58:39: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1613 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1050603/SRX1050603.20_summits.bed INFO @ Mon, 03 Jun 2019 01:58:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1052 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。