Job ID = 1300682 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:21:49 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 ) 2019-06-03T10:23:28 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 ) 2019-06-03T10:23:28 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 ) 2019-06-03T10:26:24 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 ) 2019-06-03T10:30:57 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 : 48,780,977 reads read : 48,780,977 reads written : 48,780,977 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:30 48780977 reads; of these: 48780977 (100.00%) were unpaired; of these: 11736524 (24.06%) aligned 0 times 14998882 (30.75%) aligned exactly 1 time 22045571 (45.19%) aligned >1 times 75.94% overall alignment rate Time searching: 00:21:31 Overall time: 00:21:31 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 16 files... [bam_rmdupse_core] 12132219 / 37044453 = 0.3275 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 20:04:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.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 20:04:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:04:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:04:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.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 20:04:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:04:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:04:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.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 20:04:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:04:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:04:34: 1000000 INFO @ Mon, 03 Jun 2019 20:04:37: 1000000 INFO @ Mon, 03 Jun 2019 20:04:37: 1000000 INFO @ Mon, 03 Jun 2019 20:04:42: 2000000 INFO @ Mon, 03 Jun 2019 20:04:48: 2000000 INFO @ Mon, 03 Jun 2019 20:04:48: 2000000 INFO @ Mon, 03 Jun 2019 20:04:50: 3000000 INFO @ Mon, 03 Jun 2019 20:04:59: 4000000 INFO @ Mon, 03 Jun 2019 20:04:59: 3000000 INFO @ Mon, 03 Jun 2019 20:04:59: 3000000 INFO @ Mon, 03 Jun 2019 20:05:07: 5000000 INFO @ Mon, 03 Jun 2019 20:05:10: 4000000 INFO @ Mon, 03 Jun 2019 20:05:10: 4000000 INFO @ Mon, 03 Jun 2019 20:05:15: 6000000 INFO @ Mon, 03 Jun 2019 20:05:20: 5000000 INFO @ Mon, 03 Jun 2019 20:05:21: 5000000 INFO @ Mon, 03 Jun 2019 20:05:22: 7000000 INFO @ Mon, 03 Jun 2019 20:05:30: 8000000 INFO @ Mon, 03 Jun 2019 20:05:31: 6000000 INFO @ Mon, 03 Jun 2019 20:05:32: 6000000 INFO @ Mon, 03 Jun 2019 20:05:37: 9000000 INFO @ Mon, 03 Jun 2019 20:05:41: 7000000 INFO @ Mon, 03 Jun 2019 20:05:42: 7000000 INFO @ Mon, 03 Jun 2019 20:05:45: 10000000 INFO @ Mon, 03 Jun 2019 20:05:51: 8000000 INFO @ Mon, 03 Jun 2019 20:05:52: 11000000 INFO @ Mon, 03 Jun 2019 20:05:53: 8000000 INFO @ Mon, 03 Jun 2019 20:06:00: 12000000 INFO @ Mon, 03 Jun 2019 20:06:01: 9000000 INFO @ Mon, 03 Jun 2019 20:06:03: 9000000 INFO @ Mon, 03 Jun 2019 20:06:07: 13000000 INFO @ Mon, 03 Jun 2019 20:06:11: 10000000 INFO @ Mon, 03 Jun 2019 20:06:14: 10000000 INFO @ Mon, 03 Jun 2019 20:06:15: 14000000 INFO @ Mon, 03 Jun 2019 20:06:21: 11000000 INFO @ Mon, 03 Jun 2019 20:06:22: 15000000 INFO @ Mon, 03 Jun 2019 20:06:24: 11000000 INFO @ Mon, 03 Jun 2019 20:06:30: 16000000 INFO @ Mon, 03 Jun 2019 20:06:31: 12000000 INFO @ Mon, 03 Jun 2019 20:06:35: 12000000 INFO @ Mon, 03 Jun 2019 20:06:37: 17000000 INFO @ Mon, 03 Jun 2019 20:06:41: 13000000 INFO @ Mon, 03 Jun 2019 20:06:44: 18000000 INFO @ Mon, 03 Jun 2019 20:06:45: 13000000 INFO @ Mon, 03 Jun 2019 20:06:51: 14000000 INFO @ Mon, 03 Jun 2019 20:06:52: 19000000 INFO @ Mon, 03 Jun 2019 20:06:56: 14000000 INFO @ Mon, 03 Jun 2019 20:06:59: 20000000 INFO @ Mon, 03 Jun 2019 20:07:01: 15000000 INFO @ Mon, 03 Jun 2019 20:07:06: 15000000 INFO @ Mon, 03 Jun 2019 20:07:07: 21000000 INFO @ Mon, 03 Jun 2019 20:07:11: 16000000 INFO @ Mon, 03 Jun 2019 20:07:14: 22000000 INFO @ Mon, 03 Jun 2019 20:07:17: 16000000 INFO @ Mon, 03 Jun 2019 20:07:21: 17000000 INFO @ Mon, 03 Jun 2019 20:07:22: 23000000 INFO @ Mon, 03 Jun 2019 20:07:27: 17000000 INFO @ Mon, 03 Jun 2019 20:07:29: 24000000 INFO @ Mon, 03 Jun 2019 20:07:31: 18000000 INFO @ Mon, 03 Jun 2019 20:07:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:07:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:07:36: #1 total tags in treatment: 24912234 INFO @ Mon, 03 Jun 2019 20:07:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:07:36: #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 20:07:37: #1 tags after filtering in treatment: 24912234 INFO @ Mon, 03 Jun 2019 20:07:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:07:37: #1 finished! INFO @ Mon, 03 Jun 2019 20:07:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:07:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:07:37: 18000000 INFO @ Mon, 03 Jun 2019 20:07:39: #2 number of paired peaks: 526 WARNING @ Mon, 03 Jun 2019 20:07:39: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Mon, 03 Jun 2019 20:07:39: start model_add_line... INFO @ Mon, 03 Jun 2019 20:07:39: start X-correlation... INFO @ Mon, 03 Jun 2019 20:07:39: end of X-cor INFO @ Mon, 03 Jun 2019 20:07:39: #2 finished! INFO @ Mon, 03 Jun 2019 20:07:39: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 20:07:39: #2 alternative fragment length(s) may be 2,27 bps INFO @ Mon, 03 Jun 2019 20:07:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.20_model.r WARNING @ Mon, 03 Jun 2019 20:07:39: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:07:39: #2 You may need to consider one of the other alternative d(s): 2,27 WARNING @ Mon, 03 Jun 2019 20:07:39: #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 20:07:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:07:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:07:41: 19000000 INFO @ Mon, 03 Jun 2019 20:07:48: 19000000 INFO @ Mon, 03 Jun 2019 20:07:51: 20000000 INFO @ Mon, 03 Jun 2019 20:07:58: 20000000 INFO @ Mon, 03 Jun 2019 20:08:01: 21000000 INFO @ Mon, 03 Jun 2019 20:08:09: 21000000 INFO @ Mon, 03 Jun 2019 20:08:11: 22000000 INFO @ Mon, 03 Jun 2019 20:08:19: 22000000 INFO @ Mon, 03 Jun 2019 20:08:21: 23000000 INFO @ Mon, 03 Jun 2019 20:08:30: 23000000 INFO @ Mon, 03 Jun 2019 20:08:31: 24000000 INFO @ Mon, 03 Jun 2019 20:08:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:08:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:08:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:08:39: #1 total tags in treatment: 24912234 INFO @ Mon, 03 Jun 2019 20:08:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:08:39: #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 20:08:40: #1 tags after filtering in treatment: 24912234 INFO @ Mon, 03 Jun 2019 20:08:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:08:40: #1 finished! INFO @ Mon, 03 Jun 2019 20:08:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:08:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:08:40: 24000000 INFO @ Mon, 03 Jun 2019 20:08:42: #2 number of paired peaks: 526 WARNING @ Mon, 03 Jun 2019 20:08:42: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Mon, 03 Jun 2019 20:08:42: start model_add_line... INFO @ Mon, 03 Jun 2019 20:08:42: start X-correlation... INFO @ Mon, 03 Jun 2019 20:08:42: end of X-cor INFO @ Mon, 03 Jun 2019 20:08:42: #2 finished! INFO @ Mon, 03 Jun 2019 20:08:42: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 20:08:42: #2 alternative fragment length(s) may be 2,27 bps INFO @ Mon, 03 Jun 2019 20:08:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.05_model.r WARNING @ Mon, 03 Jun 2019 20:08:42: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:08:42: #2 You may need to consider one of the other alternative d(s): 2,27 WARNING @ Mon, 03 Jun 2019 20:08:42: #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 20:08:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:08:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:08:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:08:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:08:50: #1 total tags in treatment: 24912234 INFO @ Mon, 03 Jun 2019 20:08:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:08:50: #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 20:08:50: #1 tags after filtering in treatment: 24912234 INFO @ Mon, 03 Jun 2019 20:08:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:08:50: #1 finished! INFO @ Mon, 03 Jun 2019 20:08:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:08:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:08:53: #2 number of paired peaks: 526 WARNING @ Mon, 03 Jun 2019 20:08:53: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Mon, 03 Jun 2019 20:08:53: start model_add_line... INFO @ Mon, 03 Jun 2019 20:08:53: start X-correlation... INFO @ Mon, 03 Jun 2019 20:08:53: end of X-cor INFO @ Mon, 03 Jun 2019 20:08:53: #2 finished! INFO @ Mon, 03 Jun 2019 20:08:53: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 20:08:53: #2 alternative fragment length(s) may be 2,27 bps INFO @ Mon, 03 Jun 2019 20:08:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.10_model.r WARNING @ Mon, 03 Jun 2019 20:08:53: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:08:53: #2 You may need to consider one of the other alternative d(s): 2,27 WARNING @ Mon, 03 Jun 2019 20:08:53: #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 20:08:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:08:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.20_summits.bed INFO @ Mon, 03 Jun 2019 20:08:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:09:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:09:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:09:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:09:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:09:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.05_summits.bed INFO @ Mon, 03 Jun 2019 20:09:59: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823790/SRX4823790.10_summits.bed INFO @ Mon, 03 Jun 2019 20:10:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。