Job ID = 5720341 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T14:53:05 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 ) 2020-04-15T14:53:05 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 ) 2020-04-15T14:53:05 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 : 20,409,844 reads read : 20,409,844 reads written : 20,409,844 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: 00:04:34 20409844 reads; of these: 20409844 (100.00%) were unpaired; of these: 7006598 (34.33%) aligned 0 times 11885876 (58.24%) aligned exactly 1 time 1517370 (7.43%) aligned >1 times 65.67% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:35 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] 3394952 / 13403246 = 0.2533 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 00:06:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.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 @ Thu, 16 Apr 2020 00:06:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:06:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:06:30: 1000000 INFO @ Thu, 16 Apr 2020 00:06:38: 2000000 INFO @ Thu, 16 Apr 2020 00:06:47: 3000000 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 00:06:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.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 @ Thu, 16 Apr 2020 00:06:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:06:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:06:55: 4000000 INFO @ Thu, 16 Apr 2020 00:07:03: 1000000 INFO @ Thu, 16 Apr 2020 00:07:04: 5000000 INFO @ Thu, 16 Apr 2020 00:07:12: 2000000 INFO @ Thu, 16 Apr 2020 00:07:14: 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 @ Thu, 16 Apr 2020 00:07:21: 3000000 INFO @ Thu, 16 Apr 2020 00:07:23: 7000000 INFO @ Thu, 16 Apr 2020 00:07:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.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 @ Thu, 16 Apr 2020 00:07:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:07:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:07:30: 4000000 INFO @ Thu, 16 Apr 2020 00:07:33: 8000000 INFO @ Thu, 16 Apr 2020 00:07:33: 1000000 INFO @ Thu, 16 Apr 2020 00:07:40: 5000000 INFO @ Thu, 16 Apr 2020 00:07:42: 2000000 INFO @ Thu, 16 Apr 2020 00:07:42: 9000000 INFO @ Thu, 16 Apr 2020 00:07:49: 6000000 INFO @ Thu, 16 Apr 2020 00:07:52: 3000000 INFO @ Thu, 16 Apr 2020 00:07:52: 10000000 INFO @ Thu, 16 Apr 2020 00:07:52: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:07:52: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:07:52: #1 total tags in treatment: 10008294 INFO @ Thu, 16 Apr 2020 00:07:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:07:52: #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 00:07:52: #1 tags after filtering in treatment: 10008294 INFO @ Thu, 16 Apr 2020 00:07:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:07:52: #1 finished! INFO @ Thu, 16 Apr 2020 00:07:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:07:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:07:53: #2 number of paired peaks: 4073 INFO @ Thu, 16 Apr 2020 00:07:53: start model_add_line... INFO @ Thu, 16 Apr 2020 00:07:53: start X-correlation... INFO @ Thu, 16 Apr 2020 00:07:53: end of X-cor INFO @ Thu, 16 Apr 2020 00:07:53: #2 finished! INFO @ Thu, 16 Apr 2020 00:07:53: #2 predicted fragment length is 184 bps INFO @ Thu, 16 Apr 2020 00:07:53: #2 alternative fragment length(s) may be 184 bps INFO @ Thu, 16 Apr 2020 00:07:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.05_model.r INFO @ Thu, 16 Apr 2020 00:07:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:07:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:07:58: 7000000 INFO @ Thu, 16 Apr 2020 00:08:01: 4000000 INFO @ Thu, 16 Apr 2020 00:08:08: 8000000 INFO @ Thu, 16 Apr 2020 00:08:10: 5000000 INFO @ Thu, 16 Apr 2020 00:08:17: 9000000 INFO @ Thu, 16 Apr 2020 00:08:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:08:19: 6000000 INFO @ Thu, 16 Apr 2020 00:08:26: 10000000 INFO @ Thu, 16 Apr 2020 00:08:26: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:08:26: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:08:26: #1 total tags in treatment: 10008294 INFO @ Thu, 16 Apr 2020 00:08:26: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:08:26: #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 00:08:26: #1 tags after filtering in treatment: 10008294 INFO @ Thu, 16 Apr 2020 00:08:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:08:26: #1 finished! INFO @ Thu, 16 Apr 2020 00:08:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:08:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:08:27: #2 number of paired peaks: 4073 INFO @ Thu, 16 Apr 2020 00:08:27: start model_add_line... INFO @ Thu, 16 Apr 2020 00:08:27: start X-correlation... INFO @ Thu, 16 Apr 2020 00:08:27: end of X-cor INFO @ Thu, 16 Apr 2020 00:08:27: #2 finished! INFO @ Thu, 16 Apr 2020 00:08:27: #2 predicted fragment length is 184 bps INFO @ Thu, 16 Apr 2020 00:08:27: #2 alternative fragment length(s) may be 184 bps INFO @ Thu, 16 Apr 2020 00:08:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.10_model.r INFO @ Thu, 16 Apr 2020 00:08:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:08:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:08:28: 7000000 INFO @ Thu, 16 Apr 2020 00:08:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:08:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:08:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.05_summits.bed INFO @ Thu, 16 Apr 2020 00:08:30: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (13314 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:08:37: 8000000 INFO @ Thu, 16 Apr 2020 00:08:46: 9000000 INFO @ Thu, 16 Apr 2020 00:08:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:08:54: 10000000 INFO @ Thu, 16 Apr 2020 00:08:54: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:08:54: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:08:54: #1 total tags in treatment: 10008294 INFO @ Thu, 16 Apr 2020 00:08:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:08:54: #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 00:08:54: #1 tags after filtering in treatment: 10008294 INFO @ Thu, 16 Apr 2020 00:08:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:08:54: #1 finished! INFO @ Thu, 16 Apr 2020 00:08:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:08:55: #2 number of paired peaks: 4073 INFO @ Thu, 16 Apr 2020 00:08:55: start model_add_line... INFO @ Thu, 16 Apr 2020 00:08:55: start X-correlation... INFO @ Thu, 16 Apr 2020 00:08:55: end of X-cor INFO @ Thu, 16 Apr 2020 00:08:55: #2 finished! INFO @ Thu, 16 Apr 2020 00:08:55: #2 predicted fragment length is 184 bps INFO @ Thu, 16 Apr 2020 00:08:55: #2 alternative fragment length(s) may be 184 bps INFO @ Thu, 16 Apr 2020 00:08:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.20_model.r INFO @ Thu, 16 Apr 2020 00:08:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:08:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:09:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:09:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:09:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.10_summits.bed INFO @ Thu, 16 Apr 2020 00:09:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9421 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 16 Apr 2020 00:09:21: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:09:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:09:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:09:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971804/SRX7971804.20_summits.bed INFO @ Thu, 16 Apr 2020 00:09:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5107 records, 4 fields): 6 millis CompletedMACS2peakCalling