Job ID = 4178559 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T04:08:01 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 ) 2019-12-05T04:08:01 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 ) spots read : 42,424,049 reads read : 84,848,098 reads written : 42,424,049 reads 0-length : 42,424,049 rm: cannot remove ‘[DSE]RR*’: 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: 00:11:49 42424049 reads; of these: 42424049 (100.00%) were unpaired; of these: 6424276 (15.14%) aligned 0 times 30869666 (72.76%) aligned exactly 1 time 5130107 (12.09%) aligned >1 times 84.86% overall alignment rate Time searching: 00:11:49 Overall time: 00:11:49 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] 23041155 / 35999773 = 0.6400 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:38:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.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 @ Thu, 05 Dec 2019 13:38:55: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:38:55: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:39:05: 1000000 INFO @ Thu, 05 Dec 2019 13:39:14: 2000000 INFO @ Thu, 05 Dec 2019 13:39:23: 3000000 INFO @ Thu, 05 Dec 2019 13:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.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 @ Thu, 05 Dec 2019 13:39:25: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:39:25: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:39:35: 4000000 INFO @ Thu, 05 Dec 2019 13:39:40: 1000000 INFO @ Thu, 05 Dec 2019 13:39:47: 5000000 INFO @ Thu, 05 Dec 2019 13:39:50: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:39:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.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 @ Thu, 05 Dec 2019 13:39:55: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:39:55: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:39:57: 6000000 INFO @ Thu, 05 Dec 2019 13:40:00: 3000000 INFO @ Thu, 05 Dec 2019 13:40:05: 1000000 INFO @ Thu, 05 Dec 2019 13:40:08: 7000000 INFO @ Thu, 05 Dec 2019 13:40:11: 4000000 INFO @ Thu, 05 Dec 2019 13:40:15: 2000000 INFO @ Thu, 05 Dec 2019 13:40:19: 8000000 INFO @ Thu, 05 Dec 2019 13:40:22: 5000000 INFO @ Thu, 05 Dec 2019 13:40:24: 3000000 INFO @ Thu, 05 Dec 2019 13:40:29: 9000000 INFO @ Thu, 05 Dec 2019 13:40:32: 6000000 INFO @ Thu, 05 Dec 2019 13:40:33: 4000000 INFO @ Thu, 05 Dec 2019 13:40:40: 10000000 INFO @ Thu, 05 Dec 2019 13:40:43: 7000000 INFO @ Thu, 05 Dec 2019 13:40:43: 5000000 INFO @ Thu, 05 Dec 2019 13:40:51: 11000000 INFO @ Thu, 05 Dec 2019 13:40:52: 6000000 INFO @ Thu, 05 Dec 2019 13:40:52: 8000000 INFO @ Thu, 05 Dec 2019 13:41:00: 7000000 INFO @ Thu, 05 Dec 2019 13:41:01: 12000000 INFO @ Thu, 05 Dec 2019 13:41:01: 9000000 INFO @ Thu, 05 Dec 2019 13:41:08: 8000000 INFO @ Thu, 05 Dec 2019 13:41:10: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:41:10: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:41:10: #1 total tags in treatment: 12958618 INFO @ Thu, 05 Dec 2019 13:41:10: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:41:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:41:10: #1 tags after filtering in treatment: 12958618 INFO @ Thu, 05 Dec 2019 13:41:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:41:10: #1 finished! INFO @ Thu, 05 Dec 2019 13:41:10: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:41:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:41:11: #2 number of paired peaks: 359 WARNING @ Thu, 05 Dec 2019 13:41:11: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Thu, 05 Dec 2019 13:41:11: start model_add_line... INFO @ Thu, 05 Dec 2019 13:41:11: 10000000 INFO @ Thu, 05 Dec 2019 13:41:11: start X-correlation... INFO @ Thu, 05 Dec 2019 13:41:11: end of X-cor INFO @ Thu, 05 Dec 2019 13:41:11: #2 finished! INFO @ Thu, 05 Dec 2019 13:41:11: #2 predicted fragment length is 150 bps INFO @ Thu, 05 Dec 2019 13:41:11: #2 alternative fragment length(s) may be 150 bps INFO @ Thu, 05 Dec 2019 13:41:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.05_model.r INFO @ Thu, 05 Dec 2019 13:41:11: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:41:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:41:16: 9000000 INFO @ Thu, 05 Dec 2019 13:41:22: 11000000 INFO @ Thu, 05 Dec 2019 13:41:25: 10000000 INFO @ Thu, 05 Dec 2019 13:41:31: 12000000 INFO @ Thu, 05 Dec 2019 13:41:34: 11000000 INFO @ Thu, 05 Dec 2019 13:41:40: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:41:40: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:41:40: #1 total tags in treatment: 12958618 INFO @ Thu, 05 Dec 2019 13:41:40: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:41:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:41:41: #1 tags after filtering in treatment: 12958618 INFO @ Thu, 05 Dec 2019 13:41:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:41:41: #1 finished! INFO @ Thu, 05 Dec 2019 13:41:41: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:41:42: #2 number of paired peaks: 359 WARNING @ Thu, 05 Dec 2019 13:41:42: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Thu, 05 Dec 2019 13:41:42: start model_add_line... INFO @ Thu, 05 Dec 2019 13:41:42: start X-correlation... INFO @ Thu, 05 Dec 2019 13:41:42: end of X-cor INFO @ Thu, 05 Dec 2019 13:41:42: #2 finished! INFO @ Thu, 05 Dec 2019 13:41:42: #2 predicted fragment length is 150 bps INFO @ Thu, 05 Dec 2019 13:41:42: #2 alternative fragment length(s) may be 150 bps INFO @ Thu, 05 Dec 2019 13:41:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.10_model.r INFO @ Thu, 05 Dec 2019 13:41:42: 12000000 INFO @ Thu, 05 Dec 2019 13:41:44: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:41:49: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:41:50: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:41:50: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:41:50: #1 total tags in treatment: 12958618 INFO @ Thu, 05 Dec 2019 13:41:50: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:41:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:41:50: #1 tags after filtering in treatment: 12958618 INFO @ Thu, 05 Dec 2019 13:41:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:41:50: #1 finished! INFO @ Thu, 05 Dec 2019 13:41:50: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:41:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:41:51: #2 number of paired peaks: 359 WARNING @ Thu, 05 Dec 2019 13:41:51: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Thu, 05 Dec 2019 13:41:51: start model_add_line... INFO @ Thu, 05 Dec 2019 13:41:51: start X-correlation... INFO @ Thu, 05 Dec 2019 13:41:51: end of X-cor INFO @ Thu, 05 Dec 2019 13:41:51: #2 finished! INFO @ Thu, 05 Dec 2019 13:41:51: #2 predicted fragment length is 150 bps INFO @ Thu, 05 Dec 2019 13:41:51: #2 alternative fragment length(s) may be 150 bps INFO @ Thu, 05 Dec 2019 13:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.20_model.r INFO @ Thu, 05 Dec 2019 13:41:51: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:42:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:42:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:42:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.05_summits.bed INFO @ Thu, 05 Dec 2019 13:42:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5245 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:42:23: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:42:32: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:42:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:42:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:42:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.10_summits.bed INFO @ Thu, 05 Dec 2019 13:42:42: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (2861 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:42:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:42:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:42:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827831/SRX5827831.20_summits.bed INFO @ Thu, 05 Dec 2019 13:42:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1264 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。