Job ID = 1298220 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:41:52 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 ) 2019-06-03T08:44:08 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 ) 2019-06-03T08:48:21 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 ) 2019-06-03T08:48:21 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 ) 2019-06-03T08:56:29 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 ) 2019-06-03T08:58:13 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 ) 2019-06-03T09:09:33 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 : 74,367,859 reads read : 148,735,718 reads written : 148,735,718 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: 00:20:58 74367859 reads; of these: 74367859 (100.00%) were paired; of these: 73264632 (98.52%) aligned concordantly 0 times 884835 (1.19%) aligned concordantly exactly 1 time 218392 (0.29%) aligned concordantly >1 times ---- 73264632 pairs aligned concordantly 0 times; of these: 3161 (0.00%) aligned discordantly 1 time ---- 73261471 pairs aligned 0 times concordantly or discordantly; of these: 146522942 mates make up the pairs; of these: 145641624 (99.40%) aligned 0 times 349195 (0.24%) aligned exactly 1 time 532123 (0.36%) aligned >1 times 2.08% overall alignment rate Time searching: 00:20:58 Overall time: 00:20:58 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] 37388 / 1063371 = 0.0352 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 18:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.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 18:45:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:45:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.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 18:45:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:45:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.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 18:45:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:45:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:45:08: 1000000 INFO @ Mon, 03 Jun 2019 18:45:09: 1000000 INFO @ Mon, 03 Jun 2019 18:45:09: 1000000 INFO @ Mon, 03 Jun 2019 18:45:15: 2000000 INFO @ Mon, 03 Jun 2019 18:45:17: 2000000 INFO @ Mon, 03 Jun 2019 18:45:17: 2000000 INFO @ Mon, 03 Jun 2019 18:45:22: 3000000 INFO @ Mon, 03 Jun 2019 18:45:22: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 18:45:22: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 18:45:22: #1 total tags in treatment: 1065860 INFO @ Mon, 03 Jun 2019 18:45:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:45:22: #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 18:45:22: #1 tags after filtering in treatment: 1032944 INFO @ Mon, 03 Jun 2019 18:45:22: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 18:45:22: #1 finished! INFO @ Mon, 03 Jun 2019 18:45:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:45:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:45:23: #2 number of paired peaks: 1653 INFO @ Mon, 03 Jun 2019 18:45:23: start model_add_line... INFO @ Mon, 03 Jun 2019 18:45:23: start X-correlation... INFO @ Mon, 03 Jun 2019 18:45:23: end of X-cor INFO @ Mon, 03 Jun 2019 18:45:23: #2 finished! INFO @ Mon, 03 Jun 2019 18:45:23: #2 predicted fragment length is 130 bps INFO @ Mon, 03 Jun 2019 18:45:23: #2 alternative fragment length(s) may be 130,588 bps INFO @ Mon, 03 Jun 2019 18:45:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.05_model.r WARNING @ Mon, 03 Jun 2019 18:45:23: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 18:45:23: #2 You may need to consider one of the other alternative d(s): 130,588 WARNING @ Mon, 03 Jun 2019 18:45:23: #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 18:45:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:45:25: 3000000 INFO @ Mon, 03 Jun 2019 18:45:25: 3000000 INFO @ Mon, 03 Jun 2019 18:45:25: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 18:45:25: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 18:45:25: #1 total tags in treatment: 1065860 INFO @ Mon, 03 Jun 2019 18:45:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:45:25: #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 18:45:25: #1 tag size is determined as 79 bps INFO @ Mon, 03 Jun 2019 18:45:25: #1 tag size = 79 INFO @ Mon, 03 Jun 2019 18:45:25: #1 total tags in treatment: 1065860 INFO @ Mon, 03 Jun 2019 18:45:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:45:25: #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 18:45:25: #1 tags after filtering in treatment: 1032944 INFO @ Mon, 03 Jun 2019 18:45:25: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 18:45:25: #1 finished! INFO @ Mon, 03 Jun 2019 18:45:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:45:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:45:25: #1 tags after filtering in treatment: 1032944 INFO @ Mon, 03 Jun 2019 18:45:25: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 18:45:25: #1 finished! INFO @ Mon, 03 Jun 2019 18:45:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:45:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:45:25: #2 number of paired peaks: 1653 INFO @ Mon, 03 Jun 2019 18:45:25: start model_add_line... INFO @ Mon, 03 Jun 2019 18:45:25: #2 number of paired peaks: 1653 INFO @ Mon, 03 Jun 2019 18:45:25: start model_add_line... INFO @ Mon, 03 Jun 2019 18:45:25: start X-correlation... INFO @ Mon, 03 Jun 2019 18:45:25: start X-correlation... INFO @ Mon, 03 Jun 2019 18:45:25: end of X-cor INFO @ Mon, 03 Jun 2019 18:45:25: #2 finished! INFO @ Mon, 03 Jun 2019 18:45:25: #2 predicted fragment length is 130 bps INFO @ Mon, 03 Jun 2019 18:45:25: #2 alternative fragment length(s) may be 130,588 bps INFO @ Mon, 03 Jun 2019 18:45:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.20_model.r INFO @ Mon, 03 Jun 2019 18:45:25: end of X-cor INFO @ Mon, 03 Jun 2019 18:45:25: #2 finished! INFO @ Mon, 03 Jun 2019 18:45:25: #2 predicted fragment length is 130 bps INFO @ Mon, 03 Jun 2019 18:45:25: #2 alternative fragment length(s) may be 130,588 bps INFO @ Mon, 03 Jun 2019 18:45:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.10_model.r WARNING @ Mon, 03 Jun 2019 18:45:25: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 18:45:25: #2 You may need to consider one of the other alternative d(s): 130,588 WARNING @ Mon, 03 Jun 2019 18:45:25: #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 18:45:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:45:25: #3 Pre-compute pvalue-qvalue table... WARNING @ Mon, 03 Jun 2019 18:45:25: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 18:45:25: #2 You may need to consider one of the other alternative d(s): 130,588 WARNING @ Mon, 03 Jun 2019 18:45:25: #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 18:45:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:45:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:45:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:45:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.05_peaks.xls INFO @ Mon, 03 Jun 2019 18:45:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:45:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.05_summits.bed INFO @ Mon, 03 Jun 2019 18:45:28: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:45:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:45:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:45:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.20_peaks.xls INFO @ Mon, 03 Jun 2019 18:45:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:45:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.10_peaks.xls INFO @ Mon, 03 Jun 2019 18:45:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.20_summits.bed INFO @ Mon, 03 Jun 2019 18:45:30: Done! INFO @ Mon, 03 Jun 2019 18:45:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:45:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650894/SRX4650894.10_summits.bed INFO @ Mon, 03 Jun 2019 18:45:30: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (219 records, 4 fields): 2 millis pass1 - making usageList (7 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (91 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。