Job ID = 5721149 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T20:16:42 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 ) 2020-04-15T20:16:42 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 : 20,186,147 reads read : 40,372,294 reads written : 40,372,294 rm: cannot remove ‘[DSE]RR*’: 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: 00:43:18 20186147 reads; of these: 20186147 (100.00%) were paired; of these: 4504690 (22.32%) aligned concordantly 0 times 10548168 (52.25%) aligned concordantly exactly 1 time 5133289 (25.43%) aligned concordantly >1 times ---- 4504690 pairs aligned concordantly 0 times; of these: 202196 (4.49%) aligned discordantly 1 time ---- 4302494 pairs aligned 0 times concordantly or discordantly; of these: 8604988 mates make up the pairs; of these: 7834622 (91.05%) aligned 0 times 405036 (4.71%) aligned exactly 1 time 365330 (4.25%) aligned >1 times 80.59% overall alignment rate Time searching: 00:43:18 Overall time: 00:43:18 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 16 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] 1299688 / 15829180 = 0.0821 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:23:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.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 @ Thu, 16 Apr 2020 06:23:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:23:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:23:36: 1000000 INFO @ Thu, 16 Apr 2020 06:23:41: 2000000 INFO @ Thu, 16 Apr 2020 06:23:47: 3000000 INFO @ Thu, 16 Apr 2020 06:23:52: 4000000 INFO @ Thu, 16 Apr 2020 06:23:58: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.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 @ Thu, 16 Apr 2020 06:24:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:24:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:24:03: 6000000 INFO @ Thu, 16 Apr 2020 06:24:06: 1000000 INFO @ Thu, 16 Apr 2020 06:24:09: 7000000 INFO @ Thu, 16 Apr 2020 06:24:11: 2000000 INFO @ Thu, 16 Apr 2020 06:24:15: 8000000 INFO @ Thu, 16 Apr 2020 06:24:17: 3000000 INFO @ Thu, 16 Apr 2020 06:24:21: 9000000 INFO @ Thu, 16 Apr 2020 06:24:23: 4000000 INFO @ Thu, 16 Apr 2020 06:24:27: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:24:29: 5000000 INFO @ Thu, 16 Apr 2020 06:24:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.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 @ Thu, 16 Apr 2020 06:24:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:24:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:24:32: 11000000 INFO @ Thu, 16 Apr 2020 06:24:35: 6000000 INFO @ Thu, 16 Apr 2020 06:24:36: 1000000 INFO @ Thu, 16 Apr 2020 06:24:38: 12000000 INFO @ Thu, 16 Apr 2020 06:24:40: 7000000 INFO @ Thu, 16 Apr 2020 06:24:41: 2000000 INFO @ Thu, 16 Apr 2020 06:24:44: 13000000 INFO @ Thu, 16 Apr 2020 06:24:46: 3000000 INFO @ Thu, 16 Apr 2020 06:24:46: 8000000 INFO @ Thu, 16 Apr 2020 06:24:50: 14000000 INFO @ Thu, 16 Apr 2020 06:24:51: 4000000 INFO @ Thu, 16 Apr 2020 06:24:52: 9000000 INFO @ Thu, 16 Apr 2020 06:24:56: 15000000 INFO @ Thu, 16 Apr 2020 06:24:56: 5000000 INFO @ Thu, 16 Apr 2020 06:24:58: 10000000 INFO @ Thu, 16 Apr 2020 06:25:01: 16000000 INFO @ Thu, 16 Apr 2020 06:25:01: 6000000 INFO @ Thu, 16 Apr 2020 06:25:04: 11000000 INFO @ Thu, 16 Apr 2020 06:25:07: 7000000 INFO @ Thu, 16 Apr 2020 06:25:07: 17000000 INFO @ Thu, 16 Apr 2020 06:25:10: 12000000 INFO @ Thu, 16 Apr 2020 06:25:12: 8000000 INFO @ Thu, 16 Apr 2020 06:25:13: 18000000 INFO @ Thu, 16 Apr 2020 06:25:16: 13000000 INFO @ Thu, 16 Apr 2020 06:25:17: 9000000 INFO @ Thu, 16 Apr 2020 06:25:19: 19000000 INFO @ Thu, 16 Apr 2020 06:25:22: 14000000 INFO @ Thu, 16 Apr 2020 06:25:23: 10000000 INFO @ Thu, 16 Apr 2020 06:25:24: 20000000 INFO @ Thu, 16 Apr 2020 06:25:28: 15000000 INFO @ Thu, 16 Apr 2020 06:25:28: 11000000 INFO @ Thu, 16 Apr 2020 06:25:30: 21000000 INFO @ Thu, 16 Apr 2020 06:25:33: 12000000 INFO @ Thu, 16 Apr 2020 06:25:33: 16000000 INFO @ Thu, 16 Apr 2020 06:25:36: 22000000 INFO @ Thu, 16 Apr 2020 06:25:38: 13000000 INFO @ Thu, 16 Apr 2020 06:25:39: 17000000 INFO @ Thu, 16 Apr 2020 06:25:42: 23000000 INFO @ Thu, 16 Apr 2020 06:25:44: 14000000 INFO @ Thu, 16 Apr 2020 06:25:45: 18000000 INFO @ Thu, 16 Apr 2020 06:25:47: 24000000 INFO @ Thu, 16 Apr 2020 06:25:49: 15000000 INFO @ Thu, 16 Apr 2020 06:25:51: 19000000 INFO @ Thu, 16 Apr 2020 06:25:53: 25000000 INFO @ Thu, 16 Apr 2020 06:25:54: 16000000 INFO @ Thu, 16 Apr 2020 06:25:57: 20000000 INFO @ Thu, 16 Apr 2020 06:25:59: 17000000 INFO @ Thu, 16 Apr 2020 06:25:59: 26000000 INFO @ Thu, 16 Apr 2020 06:26:03: 21000000 INFO @ Thu, 16 Apr 2020 06:26:04: 18000000 INFO @ Thu, 16 Apr 2020 06:26:06: 27000000 INFO @ Thu, 16 Apr 2020 06:26:09: 22000000 INFO @ Thu, 16 Apr 2020 06:26:09: 19000000 INFO @ Thu, 16 Apr 2020 06:26:12: 28000000 INFO @ Thu, 16 Apr 2020 06:26:14: 20000000 INFO @ Thu, 16 Apr 2020 06:26:15: 23000000 INFO @ Thu, 16 Apr 2020 06:26:18: 29000000 INFO @ Thu, 16 Apr 2020 06:26:19: 21000000 INFO @ Thu, 16 Apr 2020 06:26:21: 24000000 INFO @ Thu, 16 Apr 2020 06:26:24: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:26:24: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:26:24: #1 total tags in treatment: 14385309 INFO @ Thu, 16 Apr 2020 06:26:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:26:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:26:24: #1 tags after filtering in treatment: 13487642 INFO @ Thu, 16 Apr 2020 06:26:24: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 06:26:24: #1 finished! INFO @ Thu, 16 Apr 2020 06:26:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:26:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:26:25: 22000000 INFO @ Thu, 16 Apr 2020 06:26:25: #2 number of paired peaks: 859 WARNING @ Thu, 16 Apr 2020 06:26:25: Fewer paired peaks (859) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 859 pairs to build model! INFO @ Thu, 16 Apr 2020 06:26:25: start model_add_line... INFO @ Thu, 16 Apr 2020 06:26:25: start X-correlation... INFO @ Thu, 16 Apr 2020 06:26:25: end of X-cor INFO @ Thu, 16 Apr 2020 06:26:25: #2 finished! INFO @ Thu, 16 Apr 2020 06:26:25: #2 predicted fragment length is 177 bps INFO @ Thu, 16 Apr 2020 06:26:25: #2 alternative fragment length(s) may be 177 bps INFO @ Thu, 16 Apr 2020 06:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.05_model.r INFO @ Thu, 16 Apr 2020 06:26:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:26:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:26:27: 25000000 INFO @ Thu, 16 Apr 2020 06:26:30: 23000000 INFO @ Thu, 16 Apr 2020 06:26:33: 26000000 INFO @ Thu, 16 Apr 2020 06:26:35: 24000000 INFO @ Thu, 16 Apr 2020 06:26:39: 27000000 INFO @ Thu, 16 Apr 2020 06:26:40: 25000000 INFO @ Thu, 16 Apr 2020 06:26:45: 28000000 INFO @ Thu, 16 Apr 2020 06:26:45: 26000000 INFO @ Thu, 16 Apr 2020 06:26:50: 29000000 INFO @ Thu, 16 Apr 2020 06:26:50: 27000000 INFO @ Thu, 16 Apr 2020 06:26:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:26:56: 28000000 INFO @ Thu, 16 Apr 2020 06:26:56: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:26:56: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:26:56: #1 total tags in treatment: 14385309 INFO @ Thu, 16 Apr 2020 06:26:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:26:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:26:56: #1 tags after filtering in treatment: 13487642 INFO @ Thu, 16 Apr 2020 06:26:56: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 06:26:56: #1 finished! INFO @ Thu, 16 Apr 2020 06:26:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:26:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:26:57: #2 number of paired peaks: 859 WARNING @ Thu, 16 Apr 2020 06:26:57: Fewer paired peaks (859) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 859 pairs to build model! INFO @ Thu, 16 Apr 2020 06:26:57: start model_add_line... INFO @ Thu, 16 Apr 2020 06:26:57: start X-correlation... INFO @ Thu, 16 Apr 2020 06:26:57: end of X-cor INFO @ Thu, 16 Apr 2020 06:26:57: #2 finished! INFO @ Thu, 16 Apr 2020 06:26:57: #2 predicted fragment length is 177 bps INFO @ Thu, 16 Apr 2020 06:26:57: #2 alternative fragment length(s) may be 177 bps INFO @ Thu, 16 Apr 2020 06:26:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.10_model.r INFO @ Thu, 16 Apr 2020 06:26:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:26:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:27:01: 29000000 INFO @ Thu, 16 Apr 2020 06:27:06: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:27:06: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:27:06: #1 total tags in treatment: 14385309 INFO @ Thu, 16 Apr 2020 06:27:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:27:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:27:06: #1 tags after filtering in treatment: 13487642 INFO @ Thu, 16 Apr 2020 06:27:06: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 06:27:06: #1 finished! INFO @ Thu, 16 Apr 2020 06:27:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:27:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:27:07: #2 number of paired peaks: 859 WARNING @ Thu, 16 Apr 2020 06:27:07: Fewer paired peaks (859) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 859 pairs to build model! INFO @ Thu, 16 Apr 2020 06:27:07: start model_add_line... INFO @ Thu, 16 Apr 2020 06:27:07: start X-correlation... INFO @ Thu, 16 Apr 2020 06:27:07: end of X-cor INFO @ Thu, 16 Apr 2020 06:27:07: #2 finished! INFO @ Thu, 16 Apr 2020 06:27:07: #2 predicted fragment length is 177 bps INFO @ Thu, 16 Apr 2020 06:27:07: #2 alternative fragment length(s) may be 177 bps INFO @ Thu, 16 Apr 2020 06:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.20_model.r INFO @ Thu, 16 Apr 2020 06:27:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.05_summits.bed INFO @ Thu, 16 Apr 2020 06:27:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2551 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:27:26: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:27:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:27:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:27:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:27:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.10_summits.bed INFO @ Thu, 16 Apr 2020 06:27:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1615 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:27:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:27:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:27:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708287/SRX6708287.20_summits.bed INFO @ Thu, 16 Apr 2020 06:27:51: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (880 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。