Job ID = 5721251 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T21:03:37 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 ) 2020-04-15T21:03:37 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 ) 2020-04-15T21:04:52 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 ) 2020-04-15T21:09:28 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 ) 2020-04-15T21:14:17 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 ) 2020-04-15T21:14:23 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 : 8,884,501 reads read : 17,769,002 reads written : 17,021,662 reads 0-length : 747,340 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 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) 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 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] 2 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 3 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 4 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 6 unmatched pairs [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] 1 unmatched pairs [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] 50 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1812352 / 7702431 = 0.2353 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted 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 06:45:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.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 06:45:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:45:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:45:36: 1000000 INFO @ Thu, 16 Apr 2020 06:45:42: 2000000 INFO @ Thu, 16 Apr 2020 06:45:48: 3000000 INFO @ Thu, 16 Apr 2020 06:45:53: 4000000 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 06:45:59: 5000000 INFO @ Thu, 16 Apr 2020 06:46:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.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 06:46:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:46:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:46:05: 6000000 INFO @ Thu, 16 Apr 2020 06:46:06: 1000000 INFO @ Thu, 16 Apr 2020 06:46:10: 7000000 INFO @ Thu, 16 Apr 2020 06:46:12: 2000000 INFO @ Thu, 16 Apr 2020 06:46:16: 8000000 INFO @ Thu, 16 Apr 2020 06:46:18: 3000000 INFO @ Thu, 16 Apr 2020 06:46:22: 9000000 INFO @ Thu, 16 Apr 2020 06:46:24: 4000000 INFO @ Thu, 16 Apr 2020 06:46:28: 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 06:46:30: 5000000 INFO @ Thu, 16 Apr 2020 06:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.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 06:46:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:46:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:46:33: 11000000 INFO @ Thu, 16 Apr 2020 06:46:35: 6000000 INFO @ Thu, 16 Apr 2020 06:46:36: 1000000 INFO @ Thu, 16 Apr 2020 06:46:39: 12000000 INFO @ Thu, 16 Apr 2020 06:46:41: 7000000 INFO @ Thu, 16 Apr 2020 06:46:42: 2000000 INFO @ Thu, 16 Apr 2020 06:46:43: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:46:43: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:46:43: #1 total tags in treatment: 5797619 INFO @ Thu, 16 Apr 2020 06:46:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:46:43: #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 06:46:44: #1 tags after filtering in treatment: 4978918 INFO @ Thu, 16 Apr 2020 06:46:44: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 16 Apr 2020 06:46:44: #1 finished! INFO @ Thu, 16 Apr 2020 06:46:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:46:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:46:44: #2 number of paired peaks: 4492 INFO @ Thu, 16 Apr 2020 06:46:44: start model_add_line... INFO @ Thu, 16 Apr 2020 06:46:44: start X-correlation... INFO @ Thu, 16 Apr 2020 06:46:44: end of X-cor INFO @ Thu, 16 Apr 2020 06:46:44: #2 finished! INFO @ Thu, 16 Apr 2020 06:46:44: #2 predicted fragment length is 249 bps INFO @ Thu, 16 Apr 2020 06:46:44: #2 alternative fragment length(s) may be 249 bps INFO @ Thu, 16 Apr 2020 06:46:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.05_model.r INFO @ Thu, 16 Apr 2020 06:46:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:46:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:46:47: 8000000 INFO @ Thu, 16 Apr 2020 06:46:48: 3000000 INFO @ Thu, 16 Apr 2020 06:46:52: 9000000 INFO @ Thu, 16 Apr 2020 06:46:54: 4000000 INFO @ Thu, 16 Apr 2020 06:46:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:46:58: 10000000 INFO @ Thu, 16 Apr 2020 06:46:59: 5000000 INFO @ Thu, 16 Apr 2020 06:47:04: 11000000 INFO @ Thu, 16 Apr 2020 06:47:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:47:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:47:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.05_summits.bed INFO @ Thu, 16 Apr 2020 06:47:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6570 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:47:05: 6000000 INFO @ Thu, 16 Apr 2020 06:47:10: 12000000 INFO @ Thu, 16 Apr 2020 06:47:11: 7000000 INFO @ Thu, 16 Apr 2020 06:47:14: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:47:14: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:47:14: #1 total tags in treatment: 5797619 INFO @ Thu, 16 Apr 2020 06:47:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:47:14: #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 06:47:14: #1 tags after filtering in treatment: 4978918 INFO @ Thu, 16 Apr 2020 06:47:14: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 16 Apr 2020 06:47:14: #1 finished! INFO @ Thu, 16 Apr 2020 06:47:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:47:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:47:15: #2 number of paired peaks: 4492 INFO @ Thu, 16 Apr 2020 06:47:15: start model_add_line... INFO @ Thu, 16 Apr 2020 06:47:15: start X-correlation... INFO @ Thu, 16 Apr 2020 06:47:15: end of X-cor INFO @ Thu, 16 Apr 2020 06:47:15: #2 finished! INFO @ Thu, 16 Apr 2020 06:47:15: #2 predicted fragment length is 249 bps INFO @ Thu, 16 Apr 2020 06:47:15: #2 alternative fragment length(s) may be 249 bps INFO @ Thu, 16 Apr 2020 06:47:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.10_model.r INFO @ Thu, 16 Apr 2020 06:47:15: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:47:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:47:16: 8000000 INFO @ Thu, 16 Apr 2020 06:47:22: 9000000 INFO @ Thu, 16 Apr 2020 06:47:28: 10000000 INFO @ Thu, 16 Apr 2020 06:47:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:47:34: 11000000 INFO @ Thu, 16 Apr 2020 06:47:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:47:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:47:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.10_summits.bed INFO @ Thu, 16 Apr 2020 06:47:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5034 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:47:39: 12000000 INFO @ Thu, 16 Apr 2020 06:47:43: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:47:43: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:47:43: #1 total tags in treatment: 5797619 INFO @ Thu, 16 Apr 2020 06:47:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:47:43: #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 06:47:44: #1 tags after filtering in treatment: 4978918 INFO @ Thu, 16 Apr 2020 06:47:44: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 16 Apr 2020 06:47:44: #1 finished! INFO @ Thu, 16 Apr 2020 06:47:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:47:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:47:44: #2 number of paired peaks: 4492 INFO @ Thu, 16 Apr 2020 06:47:44: start model_add_line... INFO @ Thu, 16 Apr 2020 06:47:44: start X-correlation... INFO @ Thu, 16 Apr 2020 06:47:44: end of X-cor INFO @ Thu, 16 Apr 2020 06:47:44: #2 finished! INFO @ Thu, 16 Apr 2020 06:47:44: #2 predicted fragment length is 249 bps INFO @ Thu, 16 Apr 2020 06:47:44: #2 alternative fragment length(s) may be 249 bps INFO @ Thu, 16 Apr 2020 06:47:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.20_model.r INFO @ Thu, 16 Apr 2020 06:47:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:47:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:47:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:48:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:48:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:48:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050426/SRX7050426.20_summits.bed INFO @ Thu, 16 Apr 2020 06:48:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3614 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。