Job ID = 1294911 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:40:39 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 ) 2019-06-03T01:40:39 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 ) 2019-06-03T01:40:39 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 : 17,133,552 reads read : 17,133,552 reads written : 17,133,552 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: 00:08:42 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 669207 (3.91%) aligned 0 times 11145720 (65.05%) aligned exactly 1 time 5318625 (31.04%) aligned >1 times 96.09% overall alignment rate Time searching: 00:08:42 Overall time: 00:08:42 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] 2378913 / 16464345 = 0.1445 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 11:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.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 11:01:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:01:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.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 11:01:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:01:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.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 11:01:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:01:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:01:21: 1000000 INFO @ Mon, 03 Jun 2019 11:01:22: 1000000 INFO @ Mon, 03 Jun 2019 11:01:23: 1000000 INFO @ Mon, 03 Jun 2019 11:01:28: 2000000 INFO @ Mon, 03 Jun 2019 11:01:29: 2000000 INFO @ Mon, 03 Jun 2019 11:01:33: 2000000 INFO @ Mon, 03 Jun 2019 11:01:35: 3000000 INFO @ Mon, 03 Jun 2019 11:01:37: 3000000 INFO @ Mon, 03 Jun 2019 11:01:43: 4000000 INFO @ Mon, 03 Jun 2019 11:01:43: 3000000 INFO @ Mon, 03 Jun 2019 11:01:45: 4000000 INFO @ Mon, 03 Jun 2019 11:01:51: 5000000 INFO @ Mon, 03 Jun 2019 11:01:52: 4000000 INFO @ Mon, 03 Jun 2019 11:01:53: 5000000 INFO @ Mon, 03 Jun 2019 11:01:59: 6000000 INFO @ Mon, 03 Jun 2019 11:02:02: 6000000 INFO @ Mon, 03 Jun 2019 11:02:02: 5000000 INFO @ Mon, 03 Jun 2019 11:02:07: 7000000 INFO @ Mon, 03 Jun 2019 11:02:10: 7000000 INFO @ Mon, 03 Jun 2019 11:02:11: 6000000 INFO @ Mon, 03 Jun 2019 11:02:16: 8000000 INFO @ Mon, 03 Jun 2019 11:02:18: 8000000 INFO @ Mon, 03 Jun 2019 11:02:21: 7000000 INFO @ Mon, 03 Jun 2019 11:02:24: 9000000 INFO @ Mon, 03 Jun 2019 11:02:26: 9000000 INFO @ Mon, 03 Jun 2019 11:02:30: 8000000 INFO @ Mon, 03 Jun 2019 11:02:32: 10000000 INFO @ Mon, 03 Jun 2019 11:02:35: 10000000 INFO @ Mon, 03 Jun 2019 11:02:40: 9000000 INFO @ Mon, 03 Jun 2019 11:02:41: 11000000 INFO @ Mon, 03 Jun 2019 11:02:43: 11000000 INFO @ Mon, 03 Jun 2019 11:02:49: 12000000 INFO @ Mon, 03 Jun 2019 11:02:49: 10000000 INFO @ Mon, 03 Jun 2019 11:02:51: 12000000 INFO @ Mon, 03 Jun 2019 11:02:57: 13000000 INFO @ Mon, 03 Jun 2019 11:02:59: 11000000 INFO @ Mon, 03 Jun 2019 11:03:00: 13000000 INFO @ Mon, 03 Jun 2019 11:03:06: 14000000 INFO @ Mon, 03 Jun 2019 11:03:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:03:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:03:06: #1 total tags in treatment: 14085432 INFO @ Mon, 03 Jun 2019 11:03:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:03:06: #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 11:03:07: #1 tags after filtering in treatment: 14085432 INFO @ Mon, 03 Jun 2019 11:03:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:03:07: #1 finished! INFO @ Mon, 03 Jun 2019 11:03:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:03:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:03:08: 14000000 INFO @ Mon, 03 Jun 2019 11:03:08: #2 number of paired peaks: 353 WARNING @ Mon, 03 Jun 2019 11:03:08: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Mon, 03 Jun 2019 11:03:08: start model_add_line... INFO @ Mon, 03 Jun 2019 11:03:08: start X-correlation... INFO @ Mon, 03 Jun 2019 11:03:08: end of X-cor INFO @ Mon, 03 Jun 2019 11:03:08: #2 finished! INFO @ Mon, 03 Jun 2019 11:03:08: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:03:08: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:03:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.10_model.r WARNING @ Mon, 03 Jun 2019 11:03:08: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:03:08: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:03:08: #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 11:03:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:03:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:03:08: 12000000 INFO @ Mon, 03 Jun 2019 11:03:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:03:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:03:08: #1 total tags in treatment: 14085432 INFO @ Mon, 03 Jun 2019 11:03:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:03:08: #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 11:03:09: #1 tags after filtering in treatment: 14085432 INFO @ Mon, 03 Jun 2019 11:03:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:03:09: #1 finished! INFO @ Mon, 03 Jun 2019 11:03:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:03:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:03:10: #2 number of paired peaks: 353 WARNING @ Mon, 03 Jun 2019 11:03:10: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Mon, 03 Jun 2019 11:03:10: start model_add_line... INFO @ Mon, 03 Jun 2019 11:03:10: start X-correlation... INFO @ Mon, 03 Jun 2019 11:03:10: end of X-cor INFO @ Mon, 03 Jun 2019 11:03:10: #2 finished! INFO @ Mon, 03 Jun 2019 11:03:10: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:03:10: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:03:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.20_model.r WARNING @ Mon, 03 Jun 2019 11:03:10: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:03:10: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:03:10: #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 11:03:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:03:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:03:18: 13000000 INFO @ Mon, 03 Jun 2019 11:03:27: 14000000 INFO @ Mon, 03 Jun 2019 11:03:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:03:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:03:28: #1 total tags in treatment: 14085432 INFO @ Mon, 03 Jun 2019 11:03:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:03:28: #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 11:03:28: #1 tags after filtering in treatment: 14085432 INFO @ Mon, 03 Jun 2019 11:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:03:28: #1 finished! INFO @ Mon, 03 Jun 2019 11:03:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:03:29: #2 number of paired peaks: 353 WARNING @ Mon, 03 Jun 2019 11:03:29: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Mon, 03 Jun 2019 11:03:29: start model_add_line... INFO @ Mon, 03 Jun 2019 11:03:29: start X-correlation... INFO @ Mon, 03 Jun 2019 11:03:29: end of X-cor INFO @ Mon, 03 Jun 2019 11:03:29: #2 finished! INFO @ Mon, 03 Jun 2019 11:03:29: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:03:29: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:03:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.05_model.r WARNING @ Mon, 03 Jun 2019 11:03:29: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:03:29: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:03:29: #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 11:03:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:03:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:03:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:03:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:04:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:04:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:04:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.10_summits.bed INFO @ Mon, 03 Jun 2019 11:04:04: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (1917 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:04:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:04:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:04:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.20_summits.bed INFO @ Mon, 03 Jun 2019 11:04:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1493 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:04:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:04:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:04:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:04:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287984/SRX287984.05_summits.bed INFO @ Mon, 03 Jun 2019 11:04:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2170 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。