Job ID = 5720245 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T13:45:33 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 ) 2020-04-15T13:51:03 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 : 21,934,311 reads read : 43,868,622 reads written : 21,934,311 reads 0-length : 21,934,311 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: 00:02:40 21934311 reads; of these: 21934311 (100.00%) were unpaired; of these: 15926235 (72.61%) aligned 0 times 5218079 (23.79%) aligned exactly 1 time 789997 (3.60%) aligned >1 times 27.39% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 3382534 / 6008076 = 0.5630 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 @ Wed, 15 Apr 2020 22:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 15 Apr 2020 22:57:29: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:57:29: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:57:35: 1000000 INFO @ Wed, 15 Apr 2020 22:57:41: 2000000 INFO @ Wed, 15 Apr 2020 22:57:44: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:57:44: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:57:44: #1 total tags in treatment: 2625542 INFO @ Wed, 15 Apr 2020 22:57:44: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:57:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:57:44: #1 tags after filtering in treatment: 2625542 INFO @ Wed, 15 Apr 2020 22:57:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:57:44: #1 finished! INFO @ Wed, 15 Apr 2020 22:57:44: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:57:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:57:44: #2 number of paired peaks: 1907 INFO @ Wed, 15 Apr 2020 22:57:44: start model_add_line... INFO @ Wed, 15 Apr 2020 22:57:44: start X-correlation... INFO @ Wed, 15 Apr 2020 22:57:44: end of X-cor INFO @ Wed, 15 Apr 2020 22:57:44: #2 finished! INFO @ Wed, 15 Apr 2020 22:57:44: #2 predicted fragment length is 131 bps INFO @ Wed, 15 Apr 2020 22:57:44: #2 alternative fragment length(s) may be 131 bps INFO @ Wed, 15 Apr 2020 22:57:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.05_model.r INFO @ Wed, 15 Apr 2020 22:57:44: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:57:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:57:51: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.05_summits.bed INFO @ Wed, 15 Apr 2020 22:57:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1566 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 @ Wed, 15 Apr 2020 22:57:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 15 Apr 2020 22:57:59: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:57:59: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:58:05: 1000000 INFO @ Wed, 15 Apr 2020 22:58:10: 2000000 INFO @ Wed, 15 Apr 2020 22:58:14: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:58:14: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:58:14: #1 total tags in treatment: 2625542 INFO @ Wed, 15 Apr 2020 22:58:14: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:58:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:58:14: #1 tags after filtering in treatment: 2625542 INFO @ Wed, 15 Apr 2020 22:58:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:58:14: #1 finished! INFO @ Wed, 15 Apr 2020 22:58:14: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:58:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:58:14: #2 number of paired peaks: 1907 INFO @ Wed, 15 Apr 2020 22:58:14: start model_add_line... INFO @ Wed, 15 Apr 2020 22:58:14: start X-correlation... INFO @ Wed, 15 Apr 2020 22:58:14: end of X-cor INFO @ Wed, 15 Apr 2020 22:58:14: #2 finished! INFO @ Wed, 15 Apr 2020 22:58:14: #2 predicted fragment length is 131 bps INFO @ Wed, 15 Apr 2020 22:58:14: #2 alternative fragment length(s) may be 131 bps INFO @ Wed, 15 Apr 2020 22:58:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.10_model.r INFO @ Wed, 15 Apr 2020 22:58:14: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:58:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:58:20: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:58:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.10_summits.bed INFO @ Wed, 15 Apr 2020 22:58:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (452 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Wed, 15 Apr 2020 22:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 15 Apr 2020 22:58:29: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:58:29: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:58:36: 1000000 INFO @ Wed, 15 Apr 2020 22:58:41: 2000000 INFO @ Wed, 15 Apr 2020 22:58:45: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:58:45: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:58:45: #1 total tags in treatment: 2625542 INFO @ Wed, 15 Apr 2020 22:58:45: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:58:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:58:45: #1 tags after filtering in treatment: 2625542 INFO @ Wed, 15 Apr 2020 22:58:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:58:45: #1 finished! INFO @ Wed, 15 Apr 2020 22:58:45: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:58:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:58:45: #2 number of paired peaks: 1907 INFO @ Wed, 15 Apr 2020 22:58:45: start model_add_line... INFO @ Wed, 15 Apr 2020 22:58:45: start X-correlation... INFO @ Wed, 15 Apr 2020 22:58:45: end of X-cor INFO @ Wed, 15 Apr 2020 22:58:45: #2 finished! INFO @ Wed, 15 Apr 2020 22:58:45: #2 predicted fragment length is 131 bps INFO @ Wed, 15 Apr 2020 22:58:45: #2 alternative fragment length(s) may be 131 bps INFO @ Wed, 15 Apr 2020 22:58:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.20_model.r INFO @ Wed, 15 Apr 2020 22:58:45: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:58:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:58:51: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:58:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:58:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:58:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7574649/SRX7574649.20_summits.bed INFO @ Wed, 15 Apr 2020 22:58:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (115 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。