Job ID = 1293416 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T15:10:15 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 : 29,645,087 reads read : 59,290,174 reads written : 59,290,174 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: 01:24:44 29645087 reads; of these: 29645087 (100.00%) were paired; of these: 8430799 (28.44%) aligned concordantly 0 times 11948369 (40.30%) aligned concordantly exactly 1 time 9265919 (31.26%) aligned concordantly >1 times ---- 8430799 pairs aligned concordantly 0 times; of these: 2790721 (33.10%) aligned discordantly 1 time ---- 5640078 pairs aligned 0 times concordantly or discordantly; of these: 11280156 mates make up the pairs; of these: 5485297 (48.63%) aligned 0 times 517976 (4.59%) aligned exactly 1 time 5276883 (46.78%) aligned >1 times 90.75% overall alignment rate Time searching: 01:24:44 Overall time: 01:24:44 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 32 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] 6701957 / 23662399 = 0.2832 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 02:16:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.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 02:16:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:16:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:16:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.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 02:16:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:16:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:16:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.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 02:16:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:16:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:16:48: 1000000 INFO @ Mon, 03 Jun 2019 02:16:48: 1000000 INFO @ Mon, 03 Jun 2019 02:16:52: 1000000 INFO @ Mon, 03 Jun 2019 02:17:01: 2000000 INFO @ Mon, 03 Jun 2019 02:17:01: 2000000 INFO @ Mon, 03 Jun 2019 02:17:08: 2000000 INFO @ Mon, 03 Jun 2019 02:17:13: 3000000 INFO @ Mon, 03 Jun 2019 02:17:14: 3000000 INFO @ Mon, 03 Jun 2019 02:17:25: 3000000 INFO @ Mon, 03 Jun 2019 02:17:25: 4000000 INFO @ Mon, 03 Jun 2019 02:17:26: 4000000 INFO @ Mon, 03 Jun 2019 02:17:37: 5000000 INFO @ Mon, 03 Jun 2019 02:17:39: 5000000 INFO @ Mon, 03 Jun 2019 02:17:41: 4000000 INFO @ Mon, 03 Jun 2019 02:17:50: 6000000 INFO @ Mon, 03 Jun 2019 02:17:52: 6000000 INFO @ Mon, 03 Jun 2019 02:17:58: 5000000 INFO @ Mon, 03 Jun 2019 02:18:02: 7000000 INFO @ Mon, 03 Jun 2019 02:18:04: 7000000 INFO @ Mon, 03 Jun 2019 02:18:14: 8000000 INFO @ Mon, 03 Jun 2019 02:18:14: 6000000 INFO @ Mon, 03 Jun 2019 02:18:17: 8000000 INFO @ Mon, 03 Jun 2019 02:18:26: 9000000 INFO @ Mon, 03 Jun 2019 02:18:29: 9000000 INFO @ Mon, 03 Jun 2019 02:18:30: 7000000 INFO @ Mon, 03 Jun 2019 02:18:38: 10000000 INFO @ Mon, 03 Jun 2019 02:18:42: 10000000 INFO @ Mon, 03 Jun 2019 02:18:47: 8000000 INFO @ Mon, 03 Jun 2019 02:18:50: 11000000 INFO @ Mon, 03 Jun 2019 02:18:54: 11000000 INFO @ Mon, 03 Jun 2019 02:19:02: 12000000 INFO @ Mon, 03 Jun 2019 02:19:03: 9000000 INFO @ Mon, 03 Jun 2019 02:19:07: 12000000 INFO @ Mon, 03 Jun 2019 02:19:14: 13000000 INFO @ Mon, 03 Jun 2019 02:19:19: 10000000 INFO @ Mon, 03 Jun 2019 02:19:20: 13000000 INFO @ Mon, 03 Jun 2019 02:19:26: 14000000 INFO @ Mon, 03 Jun 2019 02:19:32: 14000000 INFO @ Mon, 03 Jun 2019 02:19:36: 11000000 INFO @ Mon, 03 Jun 2019 02:19:38: 15000000 INFO @ Mon, 03 Jun 2019 02:19:45: 15000000 INFO @ Mon, 03 Jun 2019 02:19:50: 16000000 INFO @ Mon, 03 Jun 2019 02:19:52: 12000000 INFO @ Mon, 03 Jun 2019 02:19:57: 16000000 INFO @ Mon, 03 Jun 2019 02:20:02: 17000000 INFO @ Mon, 03 Jun 2019 02:20:08: 13000000 INFO @ Mon, 03 Jun 2019 02:20:09: 17000000 INFO @ Mon, 03 Jun 2019 02:20:14: 18000000 INFO @ Mon, 03 Jun 2019 02:20:21: 18000000 INFO @ Mon, 03 Jun 2019 02:20:25: 14000000 INFO @ Mon, 03 Jun 2019 02:20:26: 19000000 INFO @ Mon, 03 Jun 2019 02:20:33: 19000000 INFO @ Mon, 03 Jun 2019 02:20:38: 20000000 INFO @ Mon, 03 Jun 2019 02:20:41: 15000000 INFO @ Mon, 03 Jun 2019 02:20:45: 20000000 INFO @ Mon, 03 Jun 2019 02:20:50: 21000000 INFO @ Mon, 03 Jun 2019 02:20:57: 21000000 INFO @ Mon, 03 Jun 2019 02:20:57: 16000000 INFO @ Mon, 03 Jun 2019 02:21:02: 22000000 INFO @ Mon, 03 Jun 2019 02:21:09: 22000000 INFO @ Mon, 03 Jun 2019 02:21:14: 23000000 INFO @ Mon, 03 Jun 2019 02:21:14: 17000000 INFO @ Mon, 03 Jun 2019 02:21:20: 23000000 INFO @ Mon, 03 Jun 2019 02:21:25: 24000000 INFO @ Mon, 03 Jun 2019 02:21:30: 18000000 INFO @ Mon, 03 Jun 2019 02:21:32: 24000000 INFO @ Mon, 03 Jun 2019 02:21:37: 25000000 INFO @ Mon, 03 Jun 2019 02:21:43: 25000000 INFO @ Mon, 03 Jun 2019 02:21:46: 19000000 INFO @ Mon, 03 Jun 2019 02:21:48: 26000000 INFO @ Mon, 03 Jun 2019 02:21:54: 26000000 INFO @ Mon, 03 Jun 2019 02:21:59: 27000000 INFO @ Mon, 03 Jun 2019 02:22:02: 20000000 INFO @ Mon, 03 Jun 2019 02:22:05: 27000000 INFO @ Mon, 03 Jun 2019 02:22:10: 28000000 INFO @ Mon, 03 Jun 2019 02:22:16: 28000000 INFO @ Mon, 03 Jun 2019 02:22:18: 21000000 INFO @ Mon, 03 Jun 2019 02:22:21: 29000000 INFO @ Mon, 03 Jun 2019 02:22:27: 29000000 INFO @ Mon, 03 Jun 2019 02:22:32: 30000000 INFO @ Mon, 03 Jun 2019 02:22:34: 22000000 INFO @ Mon, 03 Jun 2019 02:22:38: 30000000 INFO @ Mon, 03 Jun 2019 02:22:43: 31000000 INFO @ Mon, 03 Jun 2019 02:22:49: 31000000 INFO @ Mon, 03 Jun 2019 02:22:50: 23000000 INFO @ Mon, 03 Jun 2019 02:22:54: 32000000 INFO @ Mon, 03 Jun 2019 02:23:00: 32000000 INFO @ Mon, 03 Jun 2019 02:23:05: 33000000 INFO @ Mon, 03 Jun 2019 02:23:06: 24000000 INFO @ Mon, 03 Jun 2019 02:23:11: 33000000 INFO @ Mon, 03 Jun 2019 02:23:16: 34000000 INFO @ Mon, 03 Jun 2019 02:23:22: 25000000 INFO @ Mon, 03 Jun 2019 02:23:22: 34000000 INFO @ Mon, 03 Jun 2019 02:23:28: 35000000 INFO @ Mon, 03 Jun 2019 02:23:33: 35000000 INFO @ Mon, 03 Jun 2019 02:23:37: 26000000 INFO @ Mon, 03 Jun 2019 02:23:39: 36000000 INFO @ Mon, 03 Jun 2019 02:23:45: 36000000 INFO @ Mon, 03 Jun 2019 02:23:51: 37000000 INFO @ Mon, 03 Jun 2019 02:23:51: 27000000 INFO @ Mon, 03 Jun 2019 02:23:56: 37000000 INFO @ Mon, 03 Jun 2019 02:24:02: 38000000 INFO @ Mon, 03 Jun 2019 02:24:06: 28000000 INFO @ Mon, 03 Jun 2019 02:24:08: 38000000 INFO @ Mon, 03 Jun 2019 02:24:13: 39000000 INFO @ Mon, 03 Jun 2019 02:24:19: 39000000 INFO @ Mon, 03 Jun 2019 02:24:21: 29000000 INFO @ Mon, 03 Jun 2019 02:24:25: 40000000 INFO @ Mon, 03 Jun 2019 02:24:29: #1 tag size is determined as 121 bps INFO @ Mon, 03 Jun 2019 02:24:29: #1 tag size = 121 INFO @ Mon, 03 Jun 2019 02:24:29: #1 total tags in treatment: 14806779 INFO @ Mon, 03 Jun 2019 02:24:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:24:29: #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 02:24:29: #1 tags after filtering in treatment: 11091158 INFO @ Mon, 03 Jun 2019 02:24:29: #1 Redundant rate of treatment: 0.25 INFO @ Mon, 03 Jun 2019 02:24:29: #1 finished! INFO @ Mon, 03 Jun 2019 02:24:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:24:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:24:30: 40000000 INFO @ Mon, 03 Jun 2019 02:24:31: #2 number of paired peaks: 2833 INFO @ Mon, 03 Jun 2019 02:24:31: start model_add_line... INFO @ Mon, 03 Jun 2019 02:24:31: start X-correlation... INFO @ Mon, 03 Jun 2019 02:24:31: end of X-cor INFO @ Mon, 03 Jun 2019 02:24:31: #2 finished! INFO @ Mon, 03 Jun 2019 02:24:31: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 02:24:31: #2 alternative fragment length(s) may be 138 bps INFO @ Mon, 03 Jun 2019 02:24:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.20_model.r WARNING @ Mon, 03 Jun 2019 02:24:31: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:24:31: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Mon, 03 Jun 2019 02:24:31: #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 02:24:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:24:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:24:35: #1 tag size is determined as 121 bps INFO @ Mon, 03 Jun 2019 02:24:35: #1 tag size = 121 INFO @ Mon, 03 Jun 2019 02:24:35: #1 total tags in treatment: 14806779 INFO @ Mon, 03 Jun 2019 02:24:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:24:35: #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 02:24:35: #1 tags after filtering in treatment: 11091158 INFO @ Mon, 03 Jun 2019 02:24:35: #1 Redundant rate of treatment: 0.25 INFO @ Mon, 03 Jun 2019 02:24:35: #1 finished! INFO @ Mon, 03 Jun 2019 02:24:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:24:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:24:35: 30000000 INFO @ Mon, 03 Jun 2019 02:24:36: #2 number of paired peaks: 2833 INFO @ Mon, 03 Jun 2019 02:24:36: start model_add_line... INFO @ Mon, 03 Jun 2019 02:24:36: start X-correlation... INFO @ Mon, 03 Jun 2019 02:24:36: end of X-cor INFO @ Mon, 03 Jun 2019 02:24:36: #2 finished! INFO @ Mon, 03 Jun 2019 02:24:36: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 02:24:36: #2 alternative fragment length(s) may be 138 bps INFO @ Mon, 03 Jun 2019 02:24:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.05_model.r WARNING @ Mon, 03 Jun 2019 02:24:36: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:24:36: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Mon, 03 Jun 2019 02:24:36: #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 02:24:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:24:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:24:49: 31000000 INFO @ Mon, 03 Jun 2019 02:25:03: 32000000 INFO @ Mon, 03 Jun 2019 02:25:04: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 02:25:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:25:16: 33000000 INFO @ Mon, 03 Jun 2019 02:25:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:25:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:25:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.20_summits.bed INFO @ Mon, 03 Jun 2019 02:25:20: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4864 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:25:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:25:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:25:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.05_summits.bed INFO @ Mon, 03 Jun 2019 02:25:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12692 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:25:30: 34000000 INFO @ Mon, 03 Jun 2019 02:25:43: 35000000 INFO @ Mon, 03 Jun 2019 02:25:57: 36000000 INFO @ Mon, 03 Jun 2019 02:26:11: 37000000 BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 02:26:24: 38000000 INFO @ Mon, 03 Jun 2019 02:26:38: 39000000 INFO @ Mon, 03 Jun 2019 02:26:51: 40000000 INFO @ Mon, 03 Jun 2019 02:26:56: #1 tag size is determined as 121 bps INFO @ Mon, 03 Jun 2019 02:26:56: #1 tag size = 121 INFO @ Mon, 03 Jun 2019 02:26:56: #1 total tags in treatment: 14806779 INFO @ Mon, 03 Jun 2019 02:26:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:26:56: #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 02:26:56: #1 tags after filtering in treatment: 11091158 INFO @ Mon, 03 Jun 2019 02:26:56: #1 Redundant rate of treatment: 0.25 INFO @ Mon, 03 Jun 2019 02:26:56: #1 finished! INFO @ Mon, 03 Jun 2019 02:26:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:26:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:26:58: #2 number of paired peaks: 2833 INFO @ Mon, 03 Jun 2019 02:26:58: start model_add_line... INFO @ Mon, 03 Jun 2019 02:26:58: start X-correlation... INFO @ Mon, 03 Jun 2019 02:26:58: end of X-cor INFO @ Mon, 03 Jun 2019 02:26:58: #2 finished! INFO @ Mon, 03 Jun 2019 02:26:58: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 02:26:58: #2 alternative fragment length(s) may be 138 bps INFO @ Mon, 03 Jun 2019 02:26:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.10_model.r WARNING @ Mon, 03 Jun 2019 02:26:58: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:26:58: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Mon, 03 Jun 2019 02:26:58: #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 02:26:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:27:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:27:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2145595/ERX2145595.10_summits.bed INFO @ Mon, 03 Jun 2019 02:27:49: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9128 records, 4 fields): 13 millis CompletedMACS2peakCalling