Job ID = 5790689 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T21:14:14 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 ) 2020-04-21T21:14:14 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 ) 2020-04-21T21:14:56 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 ) 2020-04-21T21:14:56 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 : 27,674,645 reads read : 27,674,645 reads written : 27,674,645 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:06 27674645 reads; of these: 27674645 (100.00%) were unpaired; of these: 6049464 (21.86%) aligned 0 times 16863398 (60.93%) aligned exactly 1 time 4761783 (17.21%) aligned >1 times 78.14% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 9939077 / 21625181 = 0.4596 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, 22 Apr 2020 06:27:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 22 Apr 2020 06:27:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:27:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:27:28: 1000000 INFO @ Wed, 22 Apr 2020 06:27:32: 2000000 INFO @ Wed, 22 Apr 2020 06:27:37: 3000000 INFO @ Wed, 22 Apr 2020 06:27:41: 4000000 INFO @ Wed, 22 Apr 2020 06:27:46: 5000000 INFO @ Wed, 22 Apr 2020 06:27:50: 6000000 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, 22 Apr 2020 06:27:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 22 Apr 2020 06:27:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:27:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:27:55: 7000000 INFO @ Wed, 22 Apr 2020 06:27:57: 1000000 INFO @ Wed, 22 Apr 2020 06:27:59: 8000000 INFO @ Wed, 22 Apr 2020 06:28:02: 2000000 INFO @ Wed, 22 Apr 2020 06:28:03: 9000000 INFO @ Wed, 22 Apr 2020 06:28:06: 3000000 INFO @ Wed, 22 Apr 2020 06:28:08: 10000000 INFO @ Wed, 22 Apr 2020 06:28:11: 4000000 INFO @ Wed, 22 Apr 2020 06:28:12: 11000000 INFO @ Wed, 22 Apr 2020 06:28:15: 5000000 INFO @ Wed, 22 Apr 2020 06:28:16: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:28:16: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:28:16: #1 total tags in treatment: 11686104 INFO @ Wed, 22 Apr 2020 06:28:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:28:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:28:16: #1 tags after filtering in treatment: 11685913 INFO @ Wed, 22 Apr 2020 06:28:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:28:16: #1 finished! INFO @ Wed, 22 Apr 2020 06:28:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:28:18: #2 number of paired peaks: 54454 INFO @ Wed, 22 Apr 2020 06:28:18: start model_add_line... INFO @ Wed, 22 Apr 2020 06:28:19: start X-correlation... INFO @ Wed, 22 Apr 2020 06:28:19: end of X-cor INFO @ Wed, 22 Apr 2020 06:28:19: #2 finished! INFO @ Wed, 22 Apr 2020 06:28:19: #2 predicted fragment length is 232 bps INFO @ Wed, 22 Apr 2020 06:28:19: #2 alternative fragment length(s) may be 232 bps INFO @ Wed, 22 Apr 2020 06:28:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.05_model.r INFO @ Wed, 22 Apr 2020 06:28:19: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:28:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:28:20: 6000000 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, 22 Apr 2020 06:28:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 22 Apr 2020 06:28:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:28:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:28:24: 7000000 INFO @ Wed, 22 Apr 2020 06:28:28: 1000000 INFO @ Wed, 22 Apr 2020 06:28:29: 8000000 INFO @ Wed, 22 Apr 2020 06:28:32: 2000000 INFO @ Wed, 22 Apr 2020 06:28:33: 9000000 INFO @ Wed, 22 Apr 2020 06:28:37: 3000000 INFO @ Wed, 22 Apr 2020 06:28:38: 10000000 INFO @ Wed, 22 Apr 2020 06:28:41: 4000000 INFO @ Wed, 22 Apr 2020 06:28:42: 11000000 INFO @ Wed, 22 Apr 2020 06:28:45: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:28:45: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:28:45: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:28:45: #1 total tags in treatment: 11686104 INFO @ Wed, 22 Apr 2020 06:28:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:28:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:28:46: 5000000 INFO @ Wed, 22 Apr 2020 06:28:46: #1 tags after filtering in treatment: 11685913 INFO @ Wed, 22 Apr 2020 06:28:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:28:46: #1 finished! INFO @ Wed, 22 Apr 2020 06:28:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:28:48: #2 number of paired peaks: 54454 INFO @ Wed, 22 Apr 2020 06:28:48: start model_add_line... INFO @ Wed, 22 Apr 2020 06:28:48: start X-correlation... INFO @ Wed, 22 Apr 2020 06:28:48: end of X-cor INFO @ Wed, 22 Apr 2020 06:28:48: #2 finished! INFO @ Wed, 22 Apr 2020 06:28:48: #2 predicted fragment length is 232 bps INFO @ Wed, 22 Apr 2020 06:28:48: #2 alternative fragment length(s) may be 232 bps INFO @ Wed, 22 Apr 2020 06:28:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.10_model.r INFO @ Wed, 22 Apr 2020 06:28:48: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:28:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:28:50: 6000000 INFO @ Wed, 22 Apr 2020 06:28:54: 7000000 INFO @ Wed, 22 Apr 2020 06:28:59: 8000000 INFO @ Wed, 22 Apr 2020 06:29:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:29:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:29:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.05_summits.bed INFO @ Wed, 22 Apr 2020 06:29:00: Done! pass1 - making usageList (109 chroms): 3 millis pass2 - checking and writing primary data (16347 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:29:03: 9000000 INFO @ Wed, 22 Apr 2020 06:29:08: 10000000 INFO @ Wed, 22 Apr 2020 06:29:12: 11000000 INFO @ Wed, 22 Apr 2020 06:29:16: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:29:16: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:29:16: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:29:16: #1 total tags in treatment: 11686104 INFO @ Wed, 22 Apr 2020 06:29:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:29:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:29:16: #1 tags after filtering in treatment: 11685913 INFO @ Wed, 22 Apr 2020 06:29:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:29:16: #1 finished! INFO @ Wed, 22 Apr 2020 06:29:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:29:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:29:18: #2 number of paired peaks: 54454 INFO @ Wed, 22 Apr 2020 06:29:18: start model_add_line... INFO @ Wed, 22 Apr 2020 06:29:18: start X-correlation... INFO @ Wed, 22 Apr 2020 06:29:18: end of X-cor INFO @ Wed, 22 Apr 2020 06:29:18: #2 finished! INFO @ Wed, 22 Apr 2020 06:29:18: #2 predicted fragment length is 232 bps INFO @ Wed, 22 Apr 2020 06:29:18: #2 alternative fragment length(s) may be 232 bps INFO @ Wed, 22 Apr 2020 06:29:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.20_model.r INFO @ Wed, 22 Apr 2020 06:29:18: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:29:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:29:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:29:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:29:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.10_summits.bed INFO @ Wed, 22 Apr 2020 06:29:29: Done! pass1 - making usageList (77 chroms): 3 millis pass2 - checking and writing primary data (11775 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:29:47: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:30:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:30:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:30:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761721/SRX5761721.20_summits.bed INFO @ Wed, 22 Apr 2020 06:30:01: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (7472 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。