Job ID = 5720346 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T14:51:52 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 ) 2020-04-15T14:51:52 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 ) 2020-04-15T14:56:08 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 ) 2020-04-15T15:00:45 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 ) 2020-04-15T15:00:45 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 ) 2020-04-15T15:00:45 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 : 28,017,931 reads read : 28,017,931 reads written : 28,017,931 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: 00:09:43 28017931 reads; of these: 28017931 (100.00%) were unpaired; of these: 695025 (2.48%) aligned 0 times 20902402 (74.60%) aligned exactly 1 time 6420504 (22.92%) aligned >1 times 97.52% overall alignment rate Time searching: 00:09:43 Overall time: 00:09:43 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 12 files... [bam_rmdupse_core] 5562789 / 27322906 = 0.2036 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 00:22:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.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 00:22:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:22:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:22:30: 1000000 INFO @ Thu, 16 Apr 2020 00:22:36: 2000000 INFO @ Thu, 16 Apr 2020 00:22:42: 3000000 INFO @ Thu, 16 Apr 2020 00:22:48: 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 @ Thu, 16 Apr 2020 00:22:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.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 00:22:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:22:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:22:54: 5000000 INFO @ Thu, 16 Apr 2020 00:23:01: 6000000 INFO @ Thu, 16 Apr 2020 00:23:01: 1000000 INFO @ Thu, 16 Apr 2020 00:23:08: 7000000 INFO @ Thu, 16 Apr 2020 00:23:09: 2000000 INFO @ Thu, 16 Apr 2020 00:23:16: 8000000 INFO @ Thu, 16 Apr 2020 00:23:16: 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 @ Thu, 16 Apr 2020 00:23:23: 9000000 INFO @ Thu, 16 Apr 2020 00:23:23: 4000000 INFO @ Thu, 16 Apr 2020 00:23:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.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 00:23:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:23:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:23:30: 10000000 INFO @ Thu, 16 Apr 2020 00:23:31: 5000000 INFO @ Thu, 16 Apr 2020 00:23:31: 1000000 INFO @ Thu, 16 Apr 2020 00:23:37: 11000000 INFO @ Thu, 16 Apr 2020 00:23:38: 6000000 INFO @ Thu, 16 Apr 2020 00:23:39: 2000000 INFO @ Thu, 16 Apr 2020 00:23:44: 12000000 INFO @ Thu, 16 Apr 2020 00:23:45: 7000000 INFO @ Thu, 16 Apr 2020 00:23:46: 3000000 INFO @ Thu, 16 Apr 2020 00:23:52: 13000000 INFO @ Thu, 16 Apr 2020 00:23:52: 8000000 INFO @ Thu, 16 Apr 2020 00:23:53: 4000000 INFO @ Thu, 16 Apr 2020 00:23:59: 14000000 INFO @ Thu, 16 Apr 2020 00:23:59: 9000000 INFO @ Thu, 16 Apr 2020 00:24:00: 5000000 INFO @ Thu, 16 Apr 2020 00:24:06: 15000000 INFO @ Thu, 16 Apr 2020 00:24:06: 10000000 INFO @ Thu, 16 Apr 2020 00:24:08: 6000000 INFO @ Thu, 16 Apr 2020 00:24:13: 16000000 INFO @ Thu, 16 Apr 2020 00:24:14: 11000000 INFO @ Thu, 16 Apr 2020 00:24:15: 7000000 INFO @ Thu, 16 Apr 2020 00:24:20: 17000000 INFO @ Thu, 16 Apr 2020 00:24:21: 12000000 INFO @ Thu, 16 Apr 2020 00:24:22: 8000000 INFO @ Thu, 16 Apr 2020 00:24:28: 18000000 INFO @ Thu, 16 Apr 2020 00:24:28: 13000000 INFO @ Thu, 16 Apr 2020 00:24:29: 9000000 INFO @ Thu, 16 Apr 2020 00:24:35: 19000000 INFO @ Thu, 16 Apr 2020 00:24:35: 14000000 INFO @ Thu, 16 Apr 2020 00:24:36: 10000000 INFO @ Thu, 16 Apr 2020 00:24:42: 20000000 INFO @ Thu, 16 Apr 2020 00:24:42: 15000000 INFO @ Thu, 16 Apr 2020 00:24:43: 11000000 INFO @ Thu, 16 Apr 2020 00:24:49: 21000000 INFO @ Thu, 16 Apr 2020 00:24:49: 16000000 INFO @ Thu, 16 Apr 2020 00:24:50: 12000000 INFO @ Thu, 16 Apr 2020 00:24:54: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:24:54: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:24:54: #1 total tags in treatment: 21760117 INFO @ Thu, 16 Apr 2020 00:24:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:24:54: #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 00:24:54: #1 tags after filtering in treatment: 21760117 INFO @ Thu, 16 Apr 2020 00:24:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:24:54: #1 finished! INFO @ Thu, 16 Apr 2020 00:24:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:24:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:24:56: #2 number of paired peaks: 287 WARNING @ Thu, 16 Apr 2020 00:24:56: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Thu, 16 Apr 2020 00:24:56: start model_add_line... INFO @ Thu, 16 Apr 2020 00:24:56: start X-correlation... INFO @ Thu, 16 Apr 2020 00:24:56: end of X-cor INFO @ Thu, 16 Apr 2020 00:24:56: #2 finished! INFO @ Thu, 16 Apr 2020 00:24:56: #2 predicted fragment length is 53 bps INFO @ Thu, 16 Apr 2020 00:24:56: #2 alternative fragment length(s) may be 1,53,570 bps INFO @ Thu, 16 Apr 2020 00:24:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.05_model.r WARNING @ Thu, 16 Apr 2020 00:24:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:24:56: #2 You may need to consider one of the other alternative d(s): 1,53,570 WARNING @ Thu, 16 Apr 2020 00:24:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:24:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:24:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:24:56: 17000000 INFO @ Thu, 16 Apr 2020 00:24:57: 13000000 INFO @ Thu, 16 Apr 2020 00:25:03: 18000000 INFO @ Thu, 16 Apr 2020 00:25:04: 14000000 INFO @ Thu, 16 Apr 2020 00:25:10: 19000000 INFO @ Thu, 16 Apr 2020 00:25:11: 15000000 INFO @ Thu, 16 Apr 2020 00:25:17: 20000000 INFO @ Thu, 16 Apr 2020 00:25:19: 16000000 INFO @ Thu, 16 Apr 2020 00:25:24: 21000000 INFO @ Thu, 16 Apr 2020 00:25:26: 17000000 INFO @ Thu, 16 Apr 2020 00:25:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:25:30: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:25:30: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:25:30: #1 total tags in treatment: 21760117 INFO @ Thu, 16 Apr 2020 00:25:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:25:30: #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 00:25:30: #1 tags after filtering in treatment: 21760117 INFO @ Thu, 16 Apr 2020 00:25:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:25:30: #1 finished! INFO @ Thu, 16 Apr 2020 00:25:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:25:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:25:31: #2 number of paired peaks: 287 WARNING @ Thu, 16 Apr 2020 00:25:31: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Thu, 16 Apr 2020 00:25:31: start model_add_line... INFO @ Thu, 16 Apr 2020 00:25:32: start X-correlation... INFO @ Thu, 16 Apr 2020 00:25:32: end of X-cor INFO @ Thu, 16 Apr 2020 00:25:32: #2 finished! INFO @ Thu, 16 Apr 2020 00:25:32: #2 predicted fragment length is 53 bps INFO @ Thu, 16 Apr 2020 00:25:32: #2 alternative fragment length(s) may be 1,53,570 bps INFO @ Thu, 16 Apr 2020 00:25:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.10_model.r WARNING @ Thu, 16 Apr 2020 00:25:32: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:25:32: #2 You may need to consider one of the other alternative d(s): 1,53,570 WARNING @ Thu, 16 Apr 2020 00:25:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:25:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:25:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:25:33: 18000000 INFO @ Thu, 16 Apr 2020 00:25:39: 19000000 INFO @ Thu, 16 Apr 2020 00:25:46: 20000000 INFO @ Thu, 16 Apr 2020 00:25:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:25:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:25:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.05_summits.bed INFO @ Thu, 16 Apr 2020 00:25:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (987 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:25:52: 21000000 INFO @ Thu, 16 Apr 2020 00:25:57: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:25:57: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:25:57: #1 total tags in treatment: 21760117 INFO @ Thu, 16 Apr 2020 00:25:57: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:25:57: #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 00:25:58: #1 tags after filtering in treatment: 21760117 INFO @ Thu, 16 Apr 2020 00:25:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:25:58: #1 finished! INFO @ Thu, 16 Apr 2020 00:25:58: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:25:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:25:59: #2 number of paired peaks: 287 WARNING @ Thu, 16 Apr 2020 00:25:59: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Thu, 16 Apr 2020 00:25:59: start model_add_line... INFO @ Thu, 16 Apr 2020 00:25:59: start X-correlation... INFO @ Thu, 16 Apr 2020 00:25:59: end of X-cor INFO @ Thu, 16 Apr 2020 00:25:59: #2 finished! INFO @ Thu, 16 Apr 2020 00:25:59: #2 predicted fragment length is 53 bps INFO @ Thu, 16 Apr 2020 00:25:59: #2 alternative fragment length(s) may be 1,53,570 bps INFO @ Thu, 16 Apr 2020 00:25:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.20_model.r WARNING @ Thu, 16 Apr 2020 00:25:59: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:25:59: #2 You may need to consider one of the other alternative d(s): 1,53,570 WARNING @ Thu, 16 Apr 2020 00:25:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:25:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:25:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:26:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:26:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:26:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:26:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.10_summits.bed INFO @ Thu, 16 Apr 2020 00:26:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:26:34: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:26:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:26:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971807/SRX7971807.20_summits.bed INFO @ Thu, 16 Apr 2020 00:26:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (162 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。