Job ID = 5790806 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T22:32:50 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 ) 2020-04-21T22:32:50 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 ) 2020-04-21T22:36:08 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 ) 2020-04-21T22:38:57 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 ) 2020-04-21T22:38:57 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 ) 2020-04-21T22:40:38 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 ) 2020-04-21T22:40:38 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 : 18,857,766 reads read : 37,715,532 reads written : 18,857,766 reads 0-length : 18,857,766 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: 00:07:01 18857766 reads; of these: 18857766 (100.00%) were unpaired; of these: 12016837 (63.72%) aligned 0 times 5004002 (26.54%) aligned exactly 1 time 1836927 (9.74%) aligned >1 times 36.28% overall alignment rate Time searching: 00:07:02 Overall time: 00:07:02 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_rmdupse_core] 369580 / 6840929 = 0.0540 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 07:52:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.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 07:52:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:52:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:52:30: 1000000 INFO @ Wed, 22 Apr 2020 07:52:37: 2000000 INFO @ Wed, 22 Apr 2020 07:52:43: 3000000 INFO @ Wed, 22 Apr 2020 07:52:49: 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, 22 Apr 2020 07:52:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.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 07:52:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:52:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:52:56: 5000000 INFO @ Wed, 22 Apr 2020 07:53:01: 1000000 INFO @ Wed, 22 Apr 2020 07:53:03: 6000000 INFO @ Wed, 22 Apr 2020 07:53:06: #1 tag size is determined as 73 bps INFO @ Wed, 22 Apr 2020 07:53:06: #1 tag size = 73 INFO @ Wed, 22 Apr 2020 07:53:06: #1 total tags in treatment: 6471349 INFO @ Wed, 22 Apr 2020 07:53:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:53:06: #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 07:53:07: #1 tags after filtering in treatment: 6471064 INFO @ Wed, 22 Apr 2020 07:53:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:53:07: #1 finished! INFO @ Wed, 22 Apr 2020 07:53:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:53:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:53:08: #2 number of paired peaks: 4855 INFO @ Wed, 22 Apr 2020 07:53:08: start model_add_line... INFO @ Wed, 22 Apr 2020 07:53:08: start X-correlation... INFO @ Wed, 22 Apr 2020 07:53:08: end of X-cor INFO @ Wed, 22 Apr 2020 07:53:08: #2 finished! INFO @ Wed, 22 Apr 2020 07:53:08: #2 predicted fragment length is 75 bps INFO @ Wed, 22 Apr 2020 07:53:08: #2 alternative fragment length(s) may be 75,236 bps INFO @ Wed, 22 Apr 2020 07:53:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.05_model.r WARNING @ Wed, 22 Apr 2020 07:53:08: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:53:08: #2 You may need to consider one of the other alternative d(s): 75,236 WARNING @ Wed, 22 Apr 2020 07:53:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:53:08: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:53:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:53:08: 2000000 INFO @ Wed, 22 Apr 2020 07:53:15: 3000000 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 07:53:21: 4000000 INFO @ Wed, 22 Apr 2020 07:53:22: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:53:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.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 07:53:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:53:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:53:28: 5000000 INFO @ Wed, 22 Apr 2020 07:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:53:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.05_summits.bed INFO @ Wed, 22 Apr 2020 07:53:29: Done! INFO @ Wed, 22 Apr 2020 07:53:32: 1000000 pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (646 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:53:36: 6000000 INFO @ Wed, 22 Apr 2020 07:53:40: #1 tag size is determined as 73 bps INFO @ Wed, 22 Apr 2020 07:53:40: #1 tag size = 73 INFO @ Wed, 22 Apr 2020 07:53:40: #1 total tags in treatment: 6471349 INFO @ Wed, 22 Apr 2020 07:53:40: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:53:40: #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 07:53:40: #1 tags after filtering in treatment: 6471064 INFO @ Wed, 22 Apr 2020 07:53:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:53:40: #1 finished! INFO @ Wed, 22 Apr 2020 07:53:40: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:53:41: 2000000 INFO @ Wed, 22 Apr 2020 07:53:41: #2 number of paired peaks: 4855 INFO @ Wed, 22 Apr 2020 07:53:41: start model_add_line... INFO @ Wed, 22 Apr 2020 07:53:41: start X-correlation... INFO @ Wed, 22 Apr 2020 07:53:41: end of X-cor INFO @ Wed, 22 Apr 2020 07:53:41: #2 finished! INFO @ Wed, 22 Apr 2020 07:53:41: #2 predicted fragment length is 75 bps INFO @ Wed, 22 Apr 2020 07:53:41: #2 alternative fragment length(s) may be 75,236 bps INFO @ Wed, 22 Apr 2020 07:53:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.10_model.r WARNING @ Wed, 22 Apr 2020 07:53:41: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:53:41: #2 You may need to consider one of the other alternative d(s): 75,236 WARNING @ Wed, 22 Apr 2020 07:53:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:53:41: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:53:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:53:49: 3000000 INFO @ Wed, 22 Apr 2020 07:53:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:53:57: 4000000 INFO @ Wed, 22 Apr 2020 07:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.10_summits.bed INFO @ Wed, 22 Apr 2020 07:54:03: Done! INFO @ Wed, 22 Apr 2020 07:54:05: 5000000 pass1 - making usageList (46 chroms): 0 millis pass2 - checking and writing primary data (390 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:54:12: 6000000 INFO @ Wed, 22 Apr 2020 07:54:16: #1 tag size is determined as 73 bps INFO @ Wed, 22 Apr 2020 07:54:16: #1 tag size = 73 INFO @ Wed, 22 Apr 2020 07:54:16: #1 total tags in treatment: 6471349 INFO @ Wed, 22 Apr 2020 07:54:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:54:16: #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 07:54:16: #1 tags after filtering in treatment: 6471064 INFO @ Wed, 22 Apr 2020 07:54:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:54:16: #1 finished! INFO @ Wed, 22 Apr 2020 07:54:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:54:17: #2 number of paired peaks: 4855 INFO @ Wed, 22 Apr 2020 07:54:17: start model_add_line... INFO @ Wed, 22 Apr 2020 07:54:17: start X-correlation... INFO @ Wed, 22 Apr 2020 07:54:17: end of X-cor INFO @ Wed, 22 Apr 2020 07:54:17: #2 finished! INFO @ Wed, 22 Apr 2020 07:54:17: #2 predicted fragment length is 75 bps INFO @ Wed, 22 Apr 2020 07:54:17: #2 alternative fragment length(s) may be 75,236 bps INFO @ Wed, 22 Apr 2020 07:54:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.20_model.r WARNING @ Wed, 22 Apr 2020 07:54:17: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:54:17: #2 You may need to consider one of the other alternative d(s): 75,236 WARNING @ Wed, 22 Apr 2020 07:54:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:54:17: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:54:17: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 07:54:31: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:54:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:54:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:54:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625168/SRX7625168.20_summits.bed INFO @ Wed, 22 Apr 2020 07:54:38: Done! BigWig に変換しました。 pass1 - making usageList (29 chroms): 0 millis pass2 - checking and writing primary data (187 records, 4 fields): 2 millis CompletedMACS2peakCalling