Job ID = 1295750 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T06:35:41 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 ) 2019-06-03T06:35:41 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 ) spots read : 18,109,269 reads read : 36,218,538 reads written : 36,218,538 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: 01:26:32 18109269 reads; of these: 18109269 (100.00%) were paired; of these: 2041738 (11.27%) aligned concordantly 0 times 12233090 (67.55%) aligned concordantly exactly 1 time 3834441 (21.17%) aligned concordantly >1 times ---- 2041738 pairs aligned concordantly 0 times; of these: 177882 (8.71%) aligned discordantly 1 time ---- 1863856 pairs aligned 0 times concordantly or discordantly; of these: 3727712 mates make up the pairs; of these: 2847466 (76.39%) aligned 0 times 341080 (9.15%) aligned exactly 1 time 539166 (14.46%) aligned >1 times 92.14% overall alignment rate Time searching: 01:26:33 Overall time: 01:26:33 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 28 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] 9098225 / 11409487 = 0.7974 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 17:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.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 17:32:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:32:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.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 17:32:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:32:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.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 17:32:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:32:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:33:09: 1000000 INFO @ Mon, 03 Jun 2019 17:33:11: 1000000 INFO @ Mon, 03 Jun 2019 17:33:11: 1000000 INFO @ Mon, 03 Jun 2019 17:33:23: 2000000 INFO @ Mon, 03 Jun 2019 17:33:27: 2000000 INFO @ Mon, 03 Jun 2019 17:33:27: 2000000 INFO @ Mon, 03 Jun 2019 17:33:37: 3000000 INFO @ Mon, 03 Jun 2019 17:33:42: 3000000 INFO @ Mon, 03 Jun 2019 17:33:42: 3000000 INFO @ Mon, 03 Jun 2019 17:33:50: 4000000 INFO @ Mon, 03 Jun 2019 17:33:58: 4000000 INFO @ Mon, 03 Jun 2019 17:33:58: 4000000 INFO @ Mon, 03 Jun 2019 17:34:03: 5000000 INFO @ Mon, 03 Jun 2019 17:34:13: 5000000 INFO @ Mon, 03 Jun 2019 17:34:13: 5000000 INFO @ Mon, 03 Jun 2019 17:34:17: 6000000 INFO @ Mon, 03 Jun 2019 17:34:28: 6000000 INFO @ Mon, 03 Jun 2019 17:34:28: 6000000 INFO @ Mon, 03 Jun 2019 17:34:30: 7000000 INFO @ Mon, 03 Jun 2019 17:34:43: 8000000 INFO @ Mon, 03 Jun 2019 17:34:43: 7000000 INFO @ Mon, 03 Jun 2019 17:34:43: 7000000 INFO @ Mon, 03 Jun 2019 17:34:55: 9000000 INFO @ Mon, 03 Jun 2019 17:34:58: 8000000 INFO @ Mon, 03 Jun 2019 17:34:58: 8000000 INFO @ Mon, 03 Jun 2019 17:35:08: 10000000 INFO @ Mon, 03 Jun 2019 17:35:14: 9000000 INFO @ Mon, 03 Jun 2019 17:35:14: 9000000 INFO @ Mon, 03 Jun 2019 17:35:21: 11000000 INFO @ Mon, 03 Jun 2019 17:35:30: 10000000 INFO @ Mon, 03 Jun 2019 17:35:30: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 17:35:36: 12000000 INFO @ Mon, 03 Jun 2019 17:35:47: 11000000 INFO @ Mon, 03 Jun 2019 17:35:47: 11000000 INFO @ Mon, 03 Jun 2019 17:35:50: 13000000 BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 17:36:04: 14000000 INFO @ Mon, 03 Jun 2019 17:36:05: 12000000 INFO @ Mon, 03 Jun 2019 17:36:05: 12000000 INFO @ Mon, 03 Jun 2019 17:36:19: 15000000 INFO @ Mon, 03 Jun 2019 17:36:21: #1 tag size is determined as 142 bps INFO @ Mon, 03 Jun 2019 17:36:21: #1 tag size = 142 INFO @ Mon, 03 Jun 2019 17:36:21: #1 total tags in treatment: 7003102 INFO @ Mon, 03 Jun 2019 17:36:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:36:21: #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 17:36:22: #1 tags after filtering in treatment: 3019112 INFO @ Mon, 03 Jun 2019 17:36:22: #1 Redundant rate of treatment: 0.57 INFO @ Mon, 03 Jun 2019 17:36:22: #1 finished! INFO @ Mon, 03 Jun 2019 17:36:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:36:22: #2 number of paired peaks: 3716 INFO @ Mon, 03 Jun 2019 17:36:22: start model_add_line... INFO @ Mon, 03 Jun 2019 17:36:22: start X-correlation... INFO @ Mon, 03 Jun 2019 17:36:22: end of X-cor INFO @ Mon, 03 Jun 2019 17:36:22: #2 finished! INFO @ Mon, 03 Jun 2019 17:36:22: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 17:36:22: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 03 Jun 2019 17:36:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.20_model.r WARNING @ Mon, 03 Jun 2019 17:36:22: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:36:22: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Mon, 03 Jun 2019 17:36:22: #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 17:36:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:36:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:36:22: 13000000 INFO @ Mon, 03 Jun 2019 17:36:23: 13000000 INFO @ Mon, 03 Jun 2019 17:36:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:36:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:36:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:36:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.20_summits.bed INFO @ Mon, 03 Jun 2019 17:36:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1374 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:36:39: 14000000 INFO @ Mon, 03 Jun 2019 17:36:40: 14000000 INFO @ Mon, 03 Jun 2019 17:36:56: 15000000 INFO @ Mon, 03 Jun 2019 17:36:56: 15000000 INFO @ Mon, 03 Jun 2019 17:36:58: #1 tag size is determined as 142 bps INFO @ Mon, 03 Jun 2019 17:36:58: #1 tag size = 142 INFO @ Mon, 03 Jun 2019 17:36:58: #1 total tags in treatment: 7003102 INFO @ Mon, 03 Jun 2019 17:36:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:36:58: #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 17:36:58: #1 tags after filtering in treatment: 3019112 INFO @ Mon, 03 Jun 2019 17:36:58: #1 Redundant rate of treatment: 0.57 INFO @ Mon, 03 Jun 2019 17:36:58: #1 finished! INFO @ Mon, 03 Jun 2019 17:36:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:36:59: #1 tag size is determined as 142 bps INFO @ Mon, 03 Jun 2019 17:36:59: #1 tag size = 142 INFO @ Mon, 03 Jun 2019 17:36:59: #1 total tags in treatment: 7003102 INFO @ Mon, 03 Jun 2019 17:36:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:36:59: #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 17:36:59: #1 tags after filtering in treatment: 3019112 INFO @ Mon, 03 Jun 2019 17:36:59: #1 Redundant rate of treatment: 0.57 INFO @ Mon, 03 Jun 2019 17:36:59: #1 finished! INFO @ Mon, 03 Jun 2019 17:36:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:36:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:36:59: #2 number of paired peaks: 3716 INFO @ Mon, 03 Jun 2019 17:36:59: start model_add_line... INFO @ Mon, 03 Jun 2019 17:36:59: start X-correlation... INFO @ Mon, 03 Jun 2019 17:36:59: end of X-cor INFO @ Mon, 03 Jun 2019 17:36:59: #2 finished! INFO @ Mon, 03 Jun 2019 17:36:59: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 17:36:59: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 03 Jun 2019 17:36:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.05_model.r WARNING @ Mon, 03 Jun 2019 17:36:59: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:36:59: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Mon, 03 Jun 2019 17:36:59: #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 17:36:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:36:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:36:59: #2 number of paired peaks: 3716 INFO @ Mon, 03 Jun 2019 17:36:59: start model_add_line... INFO @ Mon, 03 Jun 2019 17:36:59: start X-correlation... INFO @ Mon, 03 Jun 2019 17:36:59: end of X-cor INFO @ Mon, 03 Jun 2019 17:36:59: #2 finished! INFO @ Mon, 03 Jun 2019 17:36:59: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 17:36:59: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 03 Jun 2019 17:36:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.10_model.r WARNING @ Mon, 03 Jun 2019 17:36:59: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 17:36:59: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Mon, 03 Jun 2019 17:36:59: #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 17:36:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:36:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:37:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:37:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:37:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:37:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:37:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.05_summits.bed INFO @ Mon, 03 Jun 2019 17:37:15: Done! pass1 - making usageList (15 chroms): 1 millis INFO @ Mon, 03 Jun 2019 17:37:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.10_peaks.xls pass2 - checking and writing primary data (5292 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:37:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:37:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4454000/SRX4454000.10_summits.bed INFO @ Mon, 03 Jun 2019 17:37:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3005 records, 4 fields): 6 millis CompletedMACS2peakCalling