Job ID = 1294726 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:47:16 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 ) 2019-06-03T00:47:16 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 ) 2019-06-03T00:47:16 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 ) 2019-06-03T00:50:21 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 : 11,363,085 reads read : 11,363,085 reads written : 11,363,085 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: 00:04:59 11363085 reads; of these: 11363085 (100.00%) were unpaired; of these: 662136 (5.83%) aligned 0 times 7157215 (62.99%) aligned exactly 1 time 3543734 (31.19%) aligned >1 times 94.17% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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] 1421659 / 10700949 = 0.1329 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 09:59:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.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 09:59:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:59:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:59:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.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 09:59:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:59:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:59:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.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 09:59:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:59:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:59:16: 1000000 INFO @ Mon, 03 Jun 2019 09:59:16: 1000000 INFO @ Mon, 03 Jun 2019 09:59:16: 1000000 INFO @ Mon, 03 Jun 2019 09:59:24: 2000000 INFO @ Mon, 03 Jun 2019 09:59:24: 2000000 INFO @ Mon, 03 Jun 2019 09:59:24: 2000000 INFO @ Mon, 03 Jun 2019 09:59:32: 3000000 INFO @ Mon, 03 Jun 2019 09:59:32: 3000000 INFO @ Mon, 03 Jun 2019 09:59:32: 3000000 INFO @ Mon, 03 Jun 2019 09:59:40: 4000000 INFO @ Mon, 03 Jun 2019 09:59:40: 4000000 INFO @ Mon, 03 Jun 2019 09:59:40: 4000000 INFO @ Mon, 03 Jun 2019 09:59:48: 5000000 INFO @ Mon, 03 Jun 2019 09:59:48: 5000000 INFO @ Mon, 03 Jun 2019 09:59:48: 5000000 INFO @ Mon, 03 Jun 2019 09:59:55: 6000000 INFO @ Mon, 03 Jun 2019 09:59:56: 6000000 INFO @ Mon, 03 Jun 2019 09:59:56: 6000000 INFO @ Mon, 03 Jun 2019 10:00:03: 7000000 INFO @ Mon, 03 Jun 2019 10:00:04: 7000000 INFO @ Mon, 03 Jun 2019 10:00:04: 7000000 INFO @ Mon, 03 Jun 2019 10:00:11: 8000000 INFO @ Mon, 03 Jun 2019 10:00:12: 8000000 INFO @ Mon, 03 Jun 2019 10:00:12: 8000000 INFO @ Mon, 03 Jun 2019 10:00:18: 9000000 INFO @ Mon, 03 Jun 2019 10:00:20: 9000000 INFO @ Mon, 03 Jun 2019 10:00:20: 9000000 INFO @ Mon, 03 Jun 2019 10:00:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:00:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:00:21: #1 total tags in treatment: 9279290 INFO @ Mon, 03 Jun 2019 10:00:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:00:21: #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 10:00:21: #1 tags after filtering in treatment: 9279290 INFO @ Mon, 03 Jun 2019 10:00:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:00:21: #1 finished! INFO @ Mon, 03 Jun 2019 10:00:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:00:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:00:22: #2 number of paired peaks: 493 WARNING @ Mon, 03 Jun 2019 10:00:22: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Mon, 03 Jun 2019 10:00:22: start model_add_line... INFO @ Mon, 03 Jun 2019 10:00:22: start X-correlation... INFO @ Mon, 03 Jun 2019 10:00:22: end of X-cor INFO @ Mon, 03 Jun 2019 10:00:22: #2 finished! INFO @ Mon, 03 Jun 2019 10:00:22: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 10:00:22: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 10:00:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.05_model.r WARNING @ Mon, 03 Jun 2019 10:00:22: #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 10:00:22: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 10:00:22: #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 10:00:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:00:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:00:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:00:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:00:23: #1 total tags in treatment: 9279290 INFO @ Mon, 03 Jun 2019 10:00:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:00:23: #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 10:00:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:00:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:00:23: #1 total tags in treatment: 9279290 INFO @ Mon, 03 Jun 2019 10:00:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:00:23: #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 10:00:23: #1 tags after filtering in treatment: 9279290 INFO @ Mon, 03 Jun 2019 10:00:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:00:23: #1 finished! INFO @ Mon, 03 Jun 2019 10:00:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:00:23: #1 tags after filtering in treatment: 9279290 INFO @ Mon, 03 Jun 2019 10:00:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:00:23: #1 finished! INFO @ Mon, 03 Jun 2019 10:00:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:00:24: #2 number of paired peaks: 493 WARNING @ Mon, 03 Jun 2019 10:00:24: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Mon, 03 Jun 2019 10:00:24: start model_add_line... INFO @ Mon, 03 Jun 2019 10:00:24: #2 number of paired peaks: 493 WARNING @ Mon, 03 Jun 2019 10:00:24: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Mon, 03 Jun 2019 10:00:24: start model_add_line... INFO @ Mon, 03 Jun 2019 10:00:24: start X-correlation... INFO @ Mon, 03 Jun 2019 10:00:24: start X-correlation... INFO @ Mon, 03 Jun 2019 10:00:24: end of X-cor INFO @ Mon, 03 Jun 2019 10:00:24: #2 finished! INFO @ Mon, 03 Jun 2019 10:00:24: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 10:00:24: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 10:00:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.20_model.r INFO @ Mon, 03 Jun 2019 10:00:24: end of X-cor INFO @ Mon, 03 Jun 2019 10:00:24: #2 finished! INFO @ Mon, 03 Jun 2019 10:00:24: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 10:00:24: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 10:00:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.10_model.r WARNING @ Mon, 03 Jun 2019 10:00:24: #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 10:00:24: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 10:00:24: #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 10:00:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:00:24: #3 Pre-compute pvalue-qvalue table... WARNING @ Mon, 03 Jun 2019 10:00:24: #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 10:00:24: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 10:00:24: #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 10:00:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:00:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:00:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:00:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:00:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:01:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:01:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:01:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.05_summits.bed INFO @ Mon, 03 Jun 2019 10:01:01: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1913 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.20_summits.bed INFO @ Mon, 03 Jun 2019 10:01:03: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (1120 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287841/SRX287841.10_summits.bed INFO @ Mon, 03 Jun 2019 10:01:03: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1559 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。