Job ID = 5720241 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 1900-01-00T00:00:00 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 ) 2020-04-15T13:37:58 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 ) 2020-04-15T13:37:58 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 ) 2020-04-15T13:44:37 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 ) spots read : 18,438,971 reads read : 18,438,971 reads written : 18,438,971 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: 00:04:42 18438971 reads; of these: 18438971 (100.00%) were unpaired; of these: 308749 (1.67%) aligned 0 times 15444557 (83.76%) aligned exactly 1 time 2685665 (14.57%) aligned >1 times 98.33% overall alignment rate Time searching: 00:04:42 Overall time: 00:04:42 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4955171 / 18130222 = 0.2733 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 22:54:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.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 22:54:05: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:54:05: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:54:11: 1000000 INFO @ Wed, 15 Apr 2020 22:54:17: 2000000 INFO @ Wed, 15 Apr 2020 22:54:23: 3000000 INFO @ Wed, 15 Apr 2020 22:54:28: 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 @ Wed, 15 Apr 2020 22:54:34: 5000000 INFO @ Wed, 15 Apr 2020 22:54:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.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 22:54:35: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:54:35: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:54:40: 6000000 INFO @ Wed, 15 Apr 2020 22:54:41: 1000000 INFO @ Wed, 15 Apr 2020 22:54:46: 7000000 INFO @ Wed, 15 Apr 2020 22:54:47: 2000000 INFO @ Wed, 15 Apr 2020 22:54:52: 3000000 INFO @ Wed, 15 Apr 2020 22:54:52: 8000000 INFO @ Wed, 15 Apr 2020 22:54:58: 4000000 INFO @ Wed, 15 Apr 2020 22:54:58: 9000000 INFO @ Wed, 15 Apr 2020 22:55:03: 5000000 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 22:55:04: 10000000 INFO @ Wed, 15 Apr 2020 22:55:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.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 22:55:05: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:55:05: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:55:09: 6000000 INFO @ Wed, 15 Apr 2020 22:55:11: 11000000 INFO @ Wed, 15 Apr 2020 22:55:11: 1000000 INFO @ Wed, 15 Apr 2020 22:55:14: 7000000 INFO @ Wed, 15 Apr 2020 22:55:16: 2000000 INFO @ Wed, 15 Apr 2020 22:55:17: 12000000 INFO @ Wed, 15 Apr 2020 22:55:20: 8000000 INFO @ Wed, 15 Apr 2020 22:55:22: 3000000 INFO @ Wed, 15 Apr 2020 22:55:23: 13000000 INFO @ Wed, 15 Apr 2020 22:55:24: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:55:24: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:55:24: #1 total tags in treatment: 13175051 INFO @ Wed, 15 Apr 2020 22:55:24: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:55:24: #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 22:55:24: #1 tags after filtering in treatment: 13175051 INFO @ Wed, 15 Apr 2020 22:55:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:55:24: #1 finished! INFO @ Wed, 15 Apr 2020 22:55:24: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:55:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:55:25: #2 number of paired peaks: 1790 INFO @ Wed, 15 Apr 2020 22:55:25: start model_add_line... INFO @ Wed, 15 Apr 2020 22:55:26: start X-correlation... INFO @ Wed, 15 Apr 2020 22:55:26: end of X-cor INFO @ Wed, 15 Apr 2020 22:55:26: #2 finished! INFO @ Wed, 15 Apr 2020 22:55:26: #2 predicted fragment length is 169 bps INFO @ Wed, 15 Apr 2020 22:55:26: #2 alternative fragment length(s) may be 169 bps INFO @ Wed, 15 Apr 2020 22:55:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.05_model.r INFO @ Wed, 15 Apr 2020 22:55:26: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:55:27: 9000000 INFO @ Wed, 15 Apr 2020 22:55:28: 4000000 INFO @ Wed, 15 Apr 2020 22:55:33: 10000000 INFO @ Wed, 15 Apr 2020 22:55:33: 5000000 INFO @ Wed, 15 Apr 2020 22:55:38: 6000000 INFO @ Wed, 15 Apr 2020 22:55:38: 11000000 INFO @ Wed, 15 Apr 2020 22:55:44: 7000000 INFO @ Wed, 15 Apr 2020 22:55:44: 12000000 INFO @ Wed, 15 Apr 2020 22:55:49: 8000000 INFO @ Wed, 15 Apr 2020 22:55:50: 13000000 INFO @ Wed, 15 Apr 2020 22:55:51: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:55:51: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:55:51: #1 total tags in treatment: 13175051 INFO @ Wed, 15 Apr 2020 22:55:51: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:55:51: #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 22:55:51: #1 tags after filtering in treatment: 13175051 INFO @ Wed, 15 Apr 2020 22:55:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:55:51: #1 finished! INFO @ Wed, 15 Apr 2020 22:55:51: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:55:52: #2 number of paired peaks: 1790 INFO @ Wed, 15 Apr 2020 22:55:52: start model_add_line... INFO @ Wed, 15 Apr 2020 22:55:52: start X-correlation... INFO @ Wed, 15 Apr 2020 22:55:52: end of X-cor INFO @ Wed, 15 Apr 2020 22:55:52: #2 finished! INFO @ Wed, 15 Apr 2020 22:55:52: #2 predicted fragment length is 169 bps INFO @ Wed, 15 Apr 2020 22:55:52: #2 alternative fragment length(s) may be 169 bps INFO @ Wed, 15 Apr 2020 22:55:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.10_model.r INFO @ Wed, 15 Apr 2020 22:55:52: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:55:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:55:55: 9000000 INFO @ Wed, 15 Apr 2020 22:55:59: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:56:00: 10000000 INFO @ Wed, 15 Apr 2020 22:56:05: 11000000 INFO @ Wed, 15 Apr 2020 22:56:10: 12000000 INFO @ Wed, 15 Apr 2020 22:56:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:56:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:56:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.05_summits.bed INFO @ Wed, 15 Apr 2020 22:56:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5914 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:56:16: 13000000 INFO @ Wed, 15 Apr 2020 22:56:17: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:56:17: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:56:17: #1 total tags in treatment: 13175051 INFO @ Wed, 15 Apr 2020 22:56:17: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:56:17: #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 22:56:17: #1 tags after filtering in treatment: 13175051 INFO @ Wed, 15 Apr 2020 22:56:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:56:17: #1 finished! INFO @ Wed, 15 Apr 2020 22:56:17: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:56:18: #2 number of paired peaks: 1790 INFO @ Wed, 15 Apr 2020 22:56:18: start model_add_line... INFO @ Wed, 15 Apr 2020 22:56:18: start X-correlation... INFO @ Wed, 15 Apr 2020 22:56:18: end of X-cor INFO @ Wed, 15 Apr 2020 22:56:18: #2 finished! INFO @ Wed, 15 Apr 2020 22:56:18: #2 predicted fragment length is 169 bps INFO @ Wed, 15 Apr 2020 22:56:18: #2 alternative fragment length(s) may be 169 bps INFO @ Wed, 15 Apr 2020 22:56:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.20_model.r INFO @ Wed, 15 Apr 2020 22:56:18: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:56:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:56:21: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:56:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:56:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:56:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.10_summits.bed INFO @ Wed, 15 Apr 2020 22:56:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4005 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:56:48: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:57:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:57:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:57:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720175/SRX6720175.20_summits.bed INFO @ Wed, 15 Apr 2020 22:57:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2206 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。