Job ID = 1295740 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T07:12:49 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 ) 2019-06-03T07:48:51 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 ) 2019-06-03T07:49:31 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 : 50,131,828 reads read : 100,263,656 reads written : 100,263,656 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 04:12:45 50131828 reads; of these: 50131828 (100.00%) were paired; of these: 5010485 (9.99%) aligned concordantly 0 times 31986786 (63.81%) aligned concordantly exactly 1 time 13134557 (26.20%) aligned concordantly >1 times ---- 5010485 pairs aligned concordantly 0 times; of these: 35854 (0.72%) aligned discordantly 1 time ---- 4974631 pairs aligned 0 times concordantly or discordantly; of these: 9949262 mates make up the pairs; of these: 7172350 (72.09%) aligned 0 times 1293707 (13.00%) aligned exactly 1 time 1483205 (14.91%) aligned >1 times 92.85% overall alignment rate Time searching: 04:12:47 Overall time: 04:12:47 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 68 files... [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] 40935708 / 44332754 = 0.9234 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 21:47:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.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 21:47:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:47:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:47:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.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 21:47:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:47:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:47:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.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 21:47:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 21:47:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 21:47:11: 1000000 INFO @ Mon, 03 Jun 2019 21:47:11: 1000000 INFO @ Mon, 03 Jun 2019 21:47:12: 1000000 INFO @ Mon, 03 Jun 2019 21:47:22: 2000000 INFO @ Mon, 03 Jun 2019 21:47:22: 2000000 INFO @ Mon, 03 Jun 2019 21:47:24: 2000000 INFO @ Mon, 03 Jun 2019 21:47:32: 3000000 INFO @ Mon, 03 Jun 2019 21:47:34: 3000000 INFO @ Mon, 03 Jun 2019 21:47:36: 3000000 INFO @ Mon, 03 Jun 2019 21:47:43: 4000000 INFO @ Mon, 03 Jun 2019 21:47:44: 4000000 INFO @ Mon, 03 Jun 2019 21:47:47: 4000000 INFO @ Mon, 03 Jun 2019 21:47:53: 5000000 INFO @ Mon, 03 Jun 2019 21:47:55: 5000000 INFO @ Mon, 03 Jun 2019 21:47:59: 5000000 INFO @ Mon, 03 Jun 2019 21:48:04: 6000000 INFO @ Mon, 03 Jun 2019 21:48:06: 6000000 INFO @ Mon, 03 Jun 2019 21:48:11: 6000000 INFO @ Mon, 03 Jun 2019 21:48:14: 7000000 INFO @ Mon, 03 Jun 2019 21:48:17: 7000000 INFO @ Mon, 03 Jun 2019 21:48:23: 7000000 INFO @ Mon, 03 Jun 2019 21:48:26: 8000000 INFO @ Mon, 03 Jun 2019 21:48:29: 8000000 INFO @ Mon, 03 Jun 2019 21:48:34: 8000000 INFO @ Mon, 03 Jun 2019 21:48:37: 9000000 INFO @ Mon, 03 Jun 2019 21:48:41: 9000000 INFO @ Mon, 03 Jun 2019 21:48:45: 9000000 INFO @ Mon, 03 Jun 2019 21:48:47: 10000000 INFO @ Mon, 03 Jun 2019 21:48:52: 10000000 INFO @ Mon, 03 Jun 2019 21:48:56: 10000000 INFO @ Mon, 03 Jun 2019 21:48:57: 11000000 INFO @ Mon, 03 Jun 2019 21:48:59: #1 tag size is determined as 150 bps INFO @ Mon, 03 Jun 2019 21:48:59: #1 tag size = 150 INFO @ Mon, 03 Jun 2019 21:48:59: #1 total tags in treatment: 4197173 INFO @ Mon, 03 Jun 2019 21:48:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:48:59: #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 21:48:59: #1 tags after filtering in treatment: 2965202 INFO @ Mon, 03 Jun 2019 21:48:59: #1 Redundant rate of treatment: 0.29 INFO @ Mon, 03 Jun 2019 21:48:59: #1 finished! INFO @ Mon, 03 Jun 2019 21:48:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:48:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:49:00: #2 number of paired peaks: 8460 INFO @ Mon, 03 Jun 2019 21:49:00: start model_add_line... INFO @ Mon, 03 Jun 2019 21:49:00: start X-correlation... INFO @ Mon, 03 Jun 2019 21:49:00: end of X-cor INFO @ Mon, 03 Jun 2019 21:49:00: #2 finished! INFO @ Mon, 03 Jun 2019 21:49:00: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 21:49:00: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 03 Jun 2019 21:49:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.05_model.r WARNING @ Mon, 03 Jun 2019 21:49:00: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:49:00: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Mon, 03 Jun 2019 21:49:00: #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 21:49:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:49:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:49:02: 11000000 INFO @ Mon, 03 Jun 2019 21:49:04: #1 tag size is determined as 150 bps INFO @ Mon, 03 Jun 2019 21:49:04: #1 tag size = 150 INFO @ Mon, 03 Jun 2019 21:49:04: #1 total tags in treatment: 4197173 INFO @ Mon, 03 Jun 2019 21:49:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:49:04: #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 21:49:04: #1 tags after filtering in treatment: 2965202 INFO @ Mon, 03 Jun 2019 21:49:04: #1 Redundant rate of treatment: 0.29 INFO @ Mon, 03 Jun 2019 21:49:04: #1 finished! INFO @ Mon, 03 Jun 2019 21:49:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:49:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:49:05: #2 number of paired peaks: 8460 INFO @ Mon, 03 Jun 2019 21:49:05: start model_add_line... INFO @ Mon, 03 Jun 2019 21:49:05: start X-correlation... INFO @ Mon, 03 Jun 2019 21:49:05: end of X-cor INFO @ Mon, 03 Jun 2019 21:49:05: #2 finished! INFO @ Mon, 03 Jun 2019 21:49:05: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 21:49:05: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 03 Jun 2019 21:49:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.10_model.r WARNING @ Mon, 03 Jun 2019 21:49:05: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:49:05: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Mon, 03 Jun 2019 21:49:05: #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 21:49:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:49:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:49:07: 11000000 INFO @ Mon, 03 Jun 2019 21:49:09: #1 tag size is determined as 150 bps INFO @ Mon, 03 Jun 2019 21:49:09: #1 tag size = 150 INFO @ Mon, 03 Jun 2019 21:49:09: #1 total tags in treatment: 4197173 INFO @ Mon, 03 Jun 2019 21:49:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 21:49:09: #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 21:49:10: #1 tags after filtering in treatment: 2965202 INFO @ Mon, 03 Jun 2019 21:49:10: #1 Redundant rate of treatment: 0.29 INFO @ Mon, 03 Jun 2019 21:49:10: #1 finished! INFO @ Mon, 03 Jun 2019 21:49:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 21:49:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 21:49:10: #2 number of paired peaks: 8460 INFO @ Mon, 03 Jun 2019 21:49:10: start model_add_line... INFO @ Mon, 03 Jun 2019 21:49:10: start X-correlation... INFO @ Mon, 03 Jun 2019 21:49:10: end of X-cor INFO @ Mon, 03 Jun 2019 21:49:10: #2 finished! INFO @ Mon, 03 Jun 2019 21:49:10: #2 predicted fragment length is 206 bps INFO @ Mon, 03 Jun 2019 21:49:10: #2 alternative fragment length(s) may be 206 bps INFO @ Mon, 03 Jun 2019 21:49:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.20_model.r WARNING @ Mon, 03 Jun 2019 21:49:10: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 21:49:10: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Mon, 03 Jun 2019 21:49:10: #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 21:49:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 21:49:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 21:49:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:49:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:49:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.05_peaks.xls INFO @ Mon, 03 Jun 2019 21:49:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:49:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.05_summits.bed INFO @ Mon, 03 Jun 2019 21:49:17: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7596 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:49:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 21:49:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.10_peaks.xls INFO @ Mon, 03 Jun 2019 21:49:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:49:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.10_summits.bed INFO @ Mon, 03 Jun 2019 21:49:21: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5127 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 21:49:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.20_peaks.xls INFO @ Mon, 03 Jun 2019 21:49:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 21:49:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4453996/SRX4453996.20_summits.bed INFO @ Mon, 03 Jun 2019 21:49:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3238 records, 4 fields): 50 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。