Job ID = 1298321 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:22:01 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 : NET - Reading information from the socket failed ) 2019-06-03T08:22:01 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 : NET - Reading information from the socket failed ) 1900-01-00T00:00:00 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 : NET - Reading information from the socket failed ) 2019-06-03T08:29:54 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 ) 2019-06-03T08:29:54 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 ) 2019-06-03T08:30:45 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 ) 2019-06-03T08:30:45 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 ) 2019-06-03T08:33:24 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 ) 2019-06-03T08:40:02 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 : 25,931,023 reads read : 51,862,046 reads written : 51,862,046 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: 00:08:35 25931023 reads; of these: 25931023 (100.00%) were paired; of these: 25311396 (97.61%) aligned concordantly 0 times 446873 (1.72%) aligned concordantly exactly 1 time 172754 (0.67%) aligned concordantly >1 times ---- 25311396 pairs aligned concordantly 0 times; of these: 1614 (0.01%) aligned discordantly 1 time ---- 25309782 pairs aligned 0 times concordantly or discordantly; of these: 50619564 mates make up the pairs; of these: 50257848 (99.29%) aligned 0 times 140816 (0.28%) aligned exactly 1 time 220900 (0.44%) aligned >1 times 3.09% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:35 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 18267 / 611450 = 0.0299 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 17:54:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.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 17:54:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:54:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:54:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.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 17:54:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:54:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:54:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.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 17:54:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:54:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:55:06: 1000000 INFO @ Mon, 03 Jun 2019 17:55:07: 1000000 INFO @ Mon, 03 Jun 2019 17:55:09: 1000000 INFO @ Mon, 03 Jun 2019 17:55:10: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 17:55:10: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 17:55:10: #1 total tags in treatment: 601372 INFO @ Mon, 03 Jun 2019 17:55:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:55:10: #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 17:55:10: #1 tags after filtering in treatment: 590580 INFO @ Mon, 03 Jun 2019 17:55:10: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 17:55:10: #1 finished! INFO @ Mon, 03 Jun 2019 17:55:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:55:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:55:10: #2 number of paired peaks: 828 WARNING @ Mon, 03 Jun 2019 17:55:10: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Mon, 03 Jun 2019 17:55:10: start model_add_line... INFO @ Mon, 03 Jun 2019 17:55:10: start X-correlation... INFO @ Mon, 03 Jun 2019 17:55:10: end of X-cor INFO @ Mon, 03 Jun 2019 17:55:10: #2 finished! INFO @ Mon, 03 Jun 2019 17:55:10: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 17:55:10: #2 alternative fragment length(s) may be 115,581 bps INFO @ Mon, 03 Jun 2019 17:55:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.10_model.r WARNING @ Mon, 03 Jun 2019 17:55:10: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:55:10: #2 You may need to consider one of the other alternative d(s): 115,581 WARNING @ Mon, 03 Jun 2019 17:55:10: #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 17:55:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:55:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:55:12: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 17:55:12: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 17:55:12: #1 total tags in treatment: 601372 INFO @ Mon, 03 Jun 2019 17:55:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:55:12: #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 17:55:12: #1 tags after filtering in treatment: 590580 INFO @ Mon, 03 Jun 2019 17:55:12: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 17:55:12: #1 finished! INFO @ Mon, 03 Jun 2019 17:55:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:55:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:55:12: #2 number of paired peaks: 828 WARNING @ Mon, 03 Jun 2019 17:55:12: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Mon, 03 Jun 2019 17:55:12: start model_add_line... INFO @ Mon, 03 Jun 2019 17:55:12: start X-correlation... INFO @ Mon, 03 Jun 2019 17:55:12: end of X-cor INFO @ Mon, 03 Jun 2019 17:55:12: #2 finished! INFO @ Mon, 03 Jun 2019 17:55:12: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 17:55:12: #2 alternative fragment length(s) may be 115,581 bps INFO @ Mon, 03 Jun 2019 17:55:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.20_model.r WARNING @ Mon, 03 Jun 2019 17:55:12: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:55:12: #2 You may need to consider one of the other alternative d(s): 115,581 WARNING @ Mon, 03 Jun 2019 17:55:12: #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 17:55:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:55:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:55:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:55:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:55:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:55:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.10_summits.bed INFO @ Mon, 03 Jun 2019 17:55:13: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:55:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:55:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:55:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:55:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.20_summits.bed INFO @ Mon, 03 Jun 2019 17:55:15: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (33 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:55:16: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 17:55:16: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 17:55:16: #1 total tags in treatment: 601372 INFO @ Mon, 03 Jun 2019 17:55:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:55:16: #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 17:55:16: #1 tags after filtering in treatment: 590580 INFO @ Mon, 03 Jun 2019 17:55:16: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 17:55:16: #1 finished! INFO @ Mon, 03 Jun 2019 17:55:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:55:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:55:16: #2 number of paired peaks: 828 WARNING @ Mon, 03 Jun 2019 17:55:16: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Mon, 03 Jun 2019 17:55:16: start model_add_line... INFO @ Mon, 03 Jun 2019 17:55:16: start X-correlation... INFO @ Mon, 03 Jun 2019 17:55:16: end of X-cor INFO @ Mon, 03 Jun 2019 17:55:16: #2 finished! INFO @ Mon, 03 Jun 2019 17:55:16: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 17:55:16: #2 alternative fragment length(s) may be 115,581 bps INFO @ Mon, 03 Jun 2019 17:55:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.05_model.r WARNING @ Mon, 03 Jun 2019 17:55:16: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:55:16: #2 You may need to consider one of the other alternative d(s): 115,581 WARNING @ Mon, 03 Jun 2019 17:55:16: #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 17:55:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:55:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:55:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:55:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:55:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:55:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650901/SRX4650901.05_summits.bed INFO @ Mon, 03 Jun 2019 17:55:19: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (150 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。