Job ID = 1298327 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:14:14 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 ) 2019-06-03T08:14:14 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 ) 2019-06-03T08:14:14 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 ) 2019-06-03T08:14:14 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 ) 2019-06-03T08:22:01 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 ) 2019-06-03T08:24:04 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 ) 2019-06-03T08:29:54 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 ) spots read : 22,765,391 reads read : 45,530,782 reads written : 45,530,782 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: 00:07:23 22765391 reads; of these: 22765391 (100.00%) were paired; of these: 22244631 (97.71%) aligned concordantly 0 times 379219 (1.67%) aligned concordantly exactly 1 time 141541 (0.62%) aligned concordantly >1 times ---- 22244631 pairs aligned concordantly 0 times; of these: 1527 (0.01%) aligned discordantly 1 time ---- 22243104 pairs aligned 0 times concordantly or discordantly; of these: 44486208 mates make up the pairs; of these: 44144033 (99.23%) aligned 0 times 142641 (0.32%) aligned exactly 1 time 199534 (0.45%) aligned >1 times 3.05% overall alignment rate Time searching: 00:07:23 Overall time: 00:07:23 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] 13982 / 508788 = 0.0275 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 17:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.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 17:46:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:46:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.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 17:46:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:46:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.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 17:46:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:46:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:46:27: 1000000 INFO @ Mon, 03 Jun 2019 17:46:28: 1000000 INFO @ Mon, 03 Jun 2019 17:46:30: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 17:46:30: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 17:46:30: #1 total tags in treatment: 506785 INFO @ Mon, 03 Jun 2019 17:46:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:46:30: #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 17:46:30: #1 tags after filtering in treatment: 498857 INFO @ Mon, 03 Jun 2019 17:46:30: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 17:46:30: #1 finished! INFO @ Mon, 03 Jun 2019 17:46:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:46:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:46:30: #2 number of paired peaks: 828 WARNING @ Mon, 03 Jun 2019 17:46:30: 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 17:46:30: start model_add_line... INFO @ Mon, 03 Jun 2019 17:46:30: start X-correlation... INFO @ Mon, 03 Jun 2019 17:46:30: end of X-cor INFO @ Mon, 03 Jun 2019 17:46:30: #2 finished! INFO @ Mon, 03 Jun 2019 17:46:30: #2 predicted fragment length is 108 bps INFO @ Mon, 03 Jun 2019 17:46:30: #2 alternative fragment length(s) may be 108,540 bps INFO @ Mon, 03 Jun 2019 17:46:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.10_model.r WARNING @ Mon, 03 Jun 2019 17:46:30: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:46:30: #2 You may need to consider one of the other alternative d(s): 108,540 WARNING @ Mon, 03 Jun 2019 17:46:30: #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 17:46:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:46:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:46:30: 1000000 INFO @ Mon, 03 Jun 2019 17:46:31: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 17:46:31: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 17:46:31: #1 total tags in treatment: 506785 INFO @ Mon, 03 Jun 2019 17:46:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:46:31: #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 17:46:31: #1 tags after filtering in treatment: 498857 INFO @ Mon, 03 Jun 2019 17:46:31: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 17:46:31: #1 finished! INFO @ Mon, 03 Jun 2019 17:46:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:46:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:46:31: #2 number of paired peaks: 828 WARNING @ Mon, 03 Jun 2019 17:46:31: 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 17:46:31: start model_add_line... INFO @ Mon, 03 Jun 2019 17:46:31: start X-correlation... INFO @ Mon, 03 Jun 2019 17:46:31: end of X-cor INFO @ Mon, 03 Jun 2019 17:46:31: #2 finished! INFO @ Mon, 03 Jun 2019 17:46:31: #2 predicted fragment length is 108 bps INFO @ Mon, 03 Jun 2019 17:46:31: #2 alternative fragment length(s) may be 108,540 bps INFO @ Mon, 03 Jun 2019 17:46:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.05_model.r WARNING @ Mon, 03 Jun 2019 17:46:31: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:46:31: #2 You may need to consider one of the other alternative d(s): 108,540 WARNING @ Mon, 03 Jun 2019 17:46:31: #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 17:46:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:46:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:46:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:46:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:46:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.10_summits.bed INFO @ Mon, 03 Jun 2019 17:46:32: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (62 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:46:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:46:33: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 17:46:33: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 17:46:33: #1 total tags in treatment: 506785 INFO @ Mon, 03 Jun 2019 17:46:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:46:33: #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 17:46:33: #1 tags after filtering in treatment: 498857 INFO @ Mon, 03 Jun 2019 17:46:33: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 17:46:33: #1 finished! INFO @ Mon, 03 Jun 2019 17:46:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:46:33: #2 number of paired peaks: 828 WARNING @ Mon, 03 Jun 2019 17:46:33: 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 17:46:33: start model_add_line... INFO @ Mon, 03 Jun 2019 17:46:33: start X-correlation... INFO @ Mon, 03 Jun 2019 17:46:33: end of X-cor INFO @ Mon, 03 Jun 2019 17:46:33: #2 finished! INFO @ Mon, 03 Jun 2019 17:46:33: #2 predicted fragment length is 108 bps INFO @ Mon, 03 Jun 2019 17:46:33: #2 alternative fragment length(s) may be 108,540 bps INFO @ Mon, 03 Jun 2019 17:46:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.20_model.r WARNING @ Mon, 03 Jun 2019 17:46:33: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:46:33: #2 You may need to consider one of the other alternative d(s): 108,540 WARNING @ Mon, 03 Jun 2019 17:46:33: #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 17:46:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:46:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:46:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:46:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.05_summits.bed INFO @ Mon, 03 Jun 2019 17:46:33: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (120 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:46:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:46:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:46:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:46:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650902/SRX4650902.20_summits.bed INFO @ Mon, 03 Jun 2019 17:46:36: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (31 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。