Job ID = 1293674 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 ) 2019-06-02T16:31:06 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 ) spots read : 18,880,153 reads read : 18,880,153 reads written : 18,880,153 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: 00:00:01 Multiseed full-index search: 00:08:38 18880153 reads; of these: 18880153 (100.00%) were unpaired; of these: 1195207 (6.33%) aligned 0 times 12716313 (67.35%) aligned exactly 1 time 4968633 (26.32%) aligned >1 times 93.67% overall alignment rate Time searching: 00:08:39 Overall time: 00:08:39 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] 6487372 / 17684946 = 0.3668 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 01:51:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.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 01:51:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:51:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:51:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.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 01:51:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:51:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:51:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.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 01:51:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:51:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:52:07: 1000000 INFO @ Mon, 03 Jun 2019 01:52:07: 1000000 INFO @ Mon, 03 Jun 2019 01:52:08: 1000000 INFO @ Mon, 03 Jun 2019 01:52:15: 2000000 INFO @ Mon, 03 Jun 2019 01:52:15: 2000000 INFO @ Mon, 03 Jun 2019 01:52:16: 2000000 INFO @ Mon, 03 Jun 2019 01:52:23: 3000000 INFO @ Mon, 03 Jun 2019 01:52:23: 3000000 INFO @ Mon, 03 Jun 2019 01:52:23: 3000000 INFO @ Mon, 03 Jun 2019 01:52:31: 4000000 INFO @ Mon, 03 Jun 2019 01:52:31: 4000000 INFO @ Mon, 03 Jun 2019 01:52:32: 4000000 INFO @ Mon, 03 Jun 2019 01:52:39: 5000000 INFO @ Mon, 03 Jun 2019 01:52:39: 5000000 INFO @ Mon, 03 Jun 2019 01:52:39: 5000000 INFO @ Mon, 03 Jun 2019 01:52:46: 6000000 INFO @ Mon, 03 Jun 2019 01:52:46: 6000000 INFO @ Mon, 03 Jun 2019 01:52:47: 6000000 INFO @ Mon, 03 Jun 2019 01:52:53: 7000000 INFO @ Mon, 03 Jun 2019 01:52:53: 7000000 INFO @ Mon, 03 Jun 2019 01:52:55: 7000000 INFO @ Mon, 03 Jun 2019 01:53:00: 8000000 INFO @ Mon, 03 Jun 2019 01:53:01: 8000000 INFO @ Mon, 03 Jun 2019 01:53:02: 8000000 INFO @ Mon, 03 Jun 2019 01:53:08: 9000000 INFO @ Mon, 03 Jun 2019 01:53:08: 9000000 INFO @ Mon, 03 Jun 2019 01:53:10: 9000000 INFO @ Mon, 03 Jun 2019 01:53:15: 10000000 INFO @ Mon, 03 Jun 2019 01:53:15: 10000000 INFO @ Mon, 03 Jun 2019 01:53:17: 10000000 INFO @ Mon, 03 Jun 2019 01:53:22: 11000000 INFO @ Mon, 03 Jun 2019 01:53:23: 11000000 INFO @ Mon, 03 Jun 2019 01:53:24: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:53:24: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:53:24: #1 total tags in treatment: 11197574 INFO @ Mon, 03 Jun 2019 01:53:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:53:24: #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 01:53:24: #1 tags after filtering in treatment: 11197574 INFO @ Mon, 03 Jun 2019 01:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:53:24: #1 finished! INFO @ Mon, 03 Jun 2019 01:53:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:53:24: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:53:24: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:53:24: #1 total tags in treatment: 11197574 INFO @ Mon, 03 Jun 2019 01:53:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:53:24: #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 01:53:24: #1 tags after filtering in treatment: 11197574 INFO @ Mon, 03 Jun 2019 01:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:53:24: #1 finished! INFO @ Mon, 03 Jun 2019 01:53:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:53:25: 11000000 INFO @ Mon, 03 Jun 2019 01:53:25: #2 number of paired peaks: 534 WARNING @ Mon, 03 Jun 2019 01:53:25: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Mon, 03 Jun 2019 01:53:25: start model_add_line... INFO @ Mon, 03 Jun 2019 01:53:25: start X-correlation... INFO @ Mon, 03 Jun 2019 01:53:25: end of X-cor INFO @ Mon, 03 Jun 2019 01:53:25: #2 finished! INFO @ Mon, 03 Jun 2019 01:53:25: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 01:53:25: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 01:53:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.20_model.r WARNING @ Mon, 03 Jun 2019 01:53:25: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:53:25: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 01:53:25: #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 01:53:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:53:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:53:25: #2 number of paired peaks: 534 WARNING @ Mon, 03 Jun 2019 01:53:25: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Mon, 03 Jun 2019 01:53:25: start model_add_line... INFO @ Mon, 03 Jun 2019 01:53:25: start X-correlation... INFO @ Mon, 03 Jun 2019 01:53:25: end of X-cor INFO @ Mon, 03 Jun 2019 01:53:25: #2 finished! INFO @ Mon, 03 Jun 2019 01:53:25: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 01:53:25: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 01:53:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.10_model.r WARNING @ Mon, 03 Jun 2019 01:53:25: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:53:25: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 01:53:25: #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 01:53:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:53:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:53:26: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:53:26: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:53:26: #1 total tags in treatment: 11197574 INFO @ Mon, 03 Jun 2019 01:53:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:53:26: #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 01:53:26: #1 tags after filtering in treatment: 11197574 INFO @ Mon, 03 Jun 2019 01:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:53:26: #1 finished! INFO @ Mon, 03 Jun 2019 01:53:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:53:28: #2 number of paired peaks: 534 WARNING @ Mon, 03 Jun 2019 01:53:28: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Mon, 03 Jun 2019 01:53:28: start model_add_line... INFO @ Mon, 03 Jun 2019 01:53:28: start X-correlation... INFO @ Mon, 03 Jun 2019 01:53:28: end of X-cor INFO @ Mon, 03 Jun 2019 01:53:28: #2 finished! INFO @ Mon, 03 Jun 2019 01:53:28: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 01:53:28: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 01:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.05_model.r WARNING @ Mon, 03 Jun 2019 01:53:28: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:53:28: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 01:53:28: #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 01:53:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:53:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:53:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:53:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:54:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:54:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:54:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.20_summits.bed INFO @ Mon, 03 Jun 2019 01:54:11: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (1172 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.10_summits.bed INFO @ Mon, 03 Jun 2019 01:54:12: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1496 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:54:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1050602/SRX1050602.05_summits.bed INFO @ Mon, 03 Jun 2019 01:54:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1758 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。