Job ID = 1294079 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T19:33:29 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 ) 2019-06-02T19:33:29 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 : 31,443,972 reads read : 31,443,972 reads written : 31,443,972 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: 00:08:50 31443972 reads; of these: 31443972 (100.00%) were unpaired; of these: 1912148 (6.08%) aligned 0 times 23971336 (76.24%) aligned exactly 1 time 5560488 (17.68%) aligned >1 times 93.92% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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] 16496792 / 29531824 = 0.5586 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 04:59:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.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 04:59:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.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 04:59:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.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 04:59:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:16: 1000000 INFO @ Mon, 03 Jun 2019 04:59:17: 1000000 INFO @ Mon, 03 Jun 2019 04:59:17: 1000000 INFO @ Mon, 03 Jun 2019 04:59:22: 2000000 INFO @ Mon, 03 Jun 2019 04:59:24: 2000000 INFO @ Mon, 03 Jun 2019 04:59:24: 2000000 INFO @ Mon, 03 Jun 2019 04:59:28: 3000000 INFO @ Mon, 03 Jun 2019 04:59:32: 3000000 INFO @ Mon, 03 Jun 2019 04:59:32: 3000000 INFO @ Mon, 03 Jun 2019 04:59:35: 4000000 INFO @ Mon, 03 Jun 2019 04:59:39: 4000000 INFO @ Mon, 03 Jun 2019 04:59:40: 4000000 INFO @ Mon, 03 Jun 2019 04:59:41: 5000000 INFO @ Mon, 03 Jun 2019 04:59:47: 5000000 INFO @ Mon, 03 Jun 2019 04:59:47: 5000000 INFO @ Mon, 03 Jun 2019 04:59:48: 6000000 INFO @ Mon, 03 Jun 2019 04:59:54: 7000000 INFO @ Mon, 03 Jun 2019 04:59:55: 6000000 INFO @ Mon, 03 Jun 2019 04:59:55: 6000000 INFO @ Mon, 03 Jun 2019 05:00:01: 8000000 INFO @ Mon, 03 Jun 2019 05:00:02: 7000000 INFO @ Mon, 03 Jun 2019 05:00:02: 7000000 INFO @ Mon, 03 Jun 2019 05:00:07: 9000000 INFO @ Mon, 03 Jun 2019 05:00:10: 8000000 INFO @ Mon, 03 Jun 2019 05:00:10: 8000000 INFO @ Mon, 03 Jun 2019 05:00:13: 10000000 INFO @ Mon, 03 Jun 2019 05:00:17: 9000000 INFO @ Mon, 03 Jun 2019 05:00:17: 9000000 INFO @ Mon, 03 Jun 2019 05:00:20: 11000000 INFO @ Mon, 03 Jun 2019 05:00:25: 10000000 INFO @ Mon, 03 Jun 2019 05:00:25: 10000000 INFO @ Mon, 03 Jun 2019 05:00:26: 12000000 INFO @ Mon, 03 Jun 2019 05:00:32: 11000000 INFO @ Mon, 03 Jun 2019 05:00:32: 11000000 INFO @ Mon, 03 Jun 2019 05:00:33: 13000000 INFO @ Mon, 03 Jun 2019 05:00:33: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:00:33: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:00:33: #1 total tags in treatment: 13035032 INFO @ Mon, 03 Jun 2019 05:00:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:00:33: #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 05:00:33: #1 tags after filtering in treatment: 13035032 INFO @ Mon, 03 Jun 2019 05:00:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:00:33: #1 finished! INFO @ Mon, 03 Jun 2019 05:00:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:00:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:00:35: #2 number of paired peaks: 682 WARNING @ Mon, 03 Jun 2019 05:00:35: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Mon, 03 Jun 2019 05:00:35: start model_add_line... INFO @ Mon, 03 Jun 2019 05:00:35: start X-correlation... INFO @ Mon, 03 Jun 2019 05:00:35: end of X-cor INFO @ Mon, 03 Jun 2019 05:00:35: #2 finished! INFO @ Mon, 03 Jun 2019 05:00:35: #2 predicted fragment length is 64 bps INFO @ Mon, 03 Jun 2019 05:00:35: #2 alternative fragment length(s) may be 64 bps INFO @ Mon, 03 Jun 2019 05:00:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.05_model.r WARNING @ Mon, 03 Jun 2019 05:00:35: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:00:35: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Mon, 03 Jun 2019 05:00:35: #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 05:00:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:00:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:00:40: 12000000 INFO @ Mon, 03 Jun 2019 05:00:40: 12000000 INFO @ Mon, 03 Jun 2019 05:00:47: 13000000 INFO @ Mon, 03 Jun 2019 05:00:47: 13000000 INFO @ Mon, 03 Jun 2019 05:00:48: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:00:48: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:00:48: #1 total tags in treatment: 13035032 INFO @ Mon, 03 Jun 2019 05:00:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:00:48: #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 05:00:48: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:00:48: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:00:48: #1 total tags in treatment: 13035032 INFO @ Mon, 03 Jun 2019 05:00:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:00:48: #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 05:00:48: #1 tags after filtering in treatment: 13035032 INFO @ Mon, 03 Jun 2019 05:00:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:00:48: #1 finished! INFO @ Mon, 03 Jun 2019 05:00:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:00:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:00:48: #1 tags after filtering in treatment: 13035032 INFO @ Mon, 03 Jun 2019 05:00:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:00:48: #1 finished! INFO @ Mon, 03 Jun 2019 05:00:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:00:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:00:49: #2 number of paired peaks: 682 WARNING @ Mon, 03 Jun 2019 05:00:49: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Mon, 03 Jun 2019 05:00:49: start model_add_line... INFO @ Mon, 03 Jun 2019 05:00:49: #2 number of paired peaks: 682 WARNING @ Mon, 03 Jun 2019 05:00:49: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Mon, 03 Jun 2019 05:00:49: start model_add_line... INFO @ Mon, 03 Jun 2019 05:00:49: start X-correlation... INFO @ Mon, 03 Jun 2019 05:00:49: end of X-cor INFO @ Mon, 03 Jun 2019 05:00:49: #2 finished! INFO @ Mon, 03 Jun 2019 05:00:49: #2 predicted fragment length is 64 bps INFO @ Mon, 03 Jun 2019 05:00:49: #2 alternative fragment length(s) may be 64 bps INFO @ Mon, 03 Jun 2019 05:00:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.20_model.r WARNING @ Mon, 03 Jun 2019 05:00:49: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:00:49: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Mon, 03 Jun 2019 05:00:49: #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 05:00:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:00:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:00:49: start X-correlation... INFO @ Mon, 03 Jun 2019 05:00:49: end of X-cor INFO @ Mon, 03 Jun 2019 05:00:49: #2 finished! INFO @ Mon, 03 Jun 2019 05:00:49: #2 predicted fragment length is 64 bps INFO @ Mon, 03 Jun 2019 05:00:49: #2 alternative fragment length(s) may be 64 bps INFO @ Mon, 03 Jun 2019 05:00:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.10_model.r WARNING @ Mon, 03 Jun 2019 05:00:49: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:00:49: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Mon, 03 Jun 2019 05:00:49: #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 05:00:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:00:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:01:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:01:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:01:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:01:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:01:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:01:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.05_summits.bed INFO @ Mon, 03 Jun 2019 05:01:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7138 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:01:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:01:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:01:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.20_summits.bed INFO @ Mon, 03 Jun 2019 05:01:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1195 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181436/SRX181436.10_summits.bed INFO @ Mon, 03 Jun 2019 05:01:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2932 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。