Job ID = 5790818 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T22:37:15 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 ) 2020-04-21T22:38:03 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 : 2,038,029 reads read : 2,038,029 reads written : 2,038,029 2020-04-21T22:40:51 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) ) 2020-04-21T22:40:51 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) ) spots read : 1,936,135 reads read : 1,936,135 reads written : 1,936,135 spots read : 1,924,318 reads read : 1,924,318 reads written : 1,924,318 2020-04-21T22:45:44 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 ) 2020-04-21T22:45:44 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 ) 2020-04-21T22:45:44 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 : 1,852,391 reads read : 1,852,391 reads written : 1,852,391 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: 00:00:01 Multiseed full-index search: 00:01:15 7750873 reads; of these: 7750873 (100.00%) were unpaired; of these: 181873 (2.35%) aligned 0 times 6424454 (82.89%) aligned exactly 1 time 1144546 (14.77%) aligned >1 times 97.65% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 7356780 / 7569000 = 0.9720 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 07:49:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.bam'] # control file = None # effective genome size = 1.21e+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, 22 Apr 2020 07:49:42: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:49:42: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:49:44: #1 tag size is determined as 69 bps INFO @ Wed, 22 Apr 2020 07:49:44: #1 tag size = 69 INFO @ Wed, 22 Apr 2020 07:49:44: #1 total tags in treatment: 212220 INFO @ Wed, 22 Apr 2020 07:49:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:49:44: #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 07:49:44: #1 tags after filtering in treatment: 212220 INFO @ Wed, 22 Apr 2020 07:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:49:44: #1 finished! INFO @ Wed, 22 Apr 2020 07:49:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:49:44: #2 number of paired peaks: 469 WARNING @ Wed, 22 Apr 2020 07:49:44: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Wed, 22 Apr 2020 07:49:44: start model_add_line... INFO @ Wed, 22 Apr 2020 07:49:44: start X-correlation... INFO @ Wed, 22 Apr 2020 07:49:44: end of X-cor INFO @ Wed, 22 Apr 2020 07:49:44: #2 finished! INFO @ Wed, 22 Apr 2020 07:49:44: #2 predicted fragment length is 81 bps INFO @ Wed, 22 Apr 2020 07:49:44: #2 alternative fragment length(s) may be 2,81,126,167,227,247,279,283,305,370,410,474,494,525,547,571 bps INFO @ Wed, 22 Apr 2020 07:49:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.05_model.r WARNING @ Wed, 22 Apr 2020 07:49:44: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:49:44: #2 You may need to consider one of the other alternative d(s): 2,81,126,167,227,247,279,283,305,370,410,474,494,525,547,571 WARNING @ Wed, 22 Apr 2020 07:49:44: #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 07:49:44: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:49:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:49:44: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:49:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:49:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:49:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.05_summits.bed INFO @ Wed, 22 Apr 2020 07:49:44: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (71 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:50:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.bam'] # control file = None # effective genome size = 1.21e+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, 22 Apr 2020 07:50:11: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:50:11: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:50:12: #1 tag size is determined as 69 bps INFO @ Wed, 22 Apr 2020 07:50:12: #1 tag size = 69 INFO @ Wed, 22 Apr 2020 07:50:12: #1 total tags in treatment: 212220 INFO @ Wed, 22 Apr 2020 07:50:12: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:50:12: #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 07:50:12: #1 tags after filtering in treatment: 212220 INFO @ Wed, 22 Apr 2020 07:50:12: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:50:12: #1 finished! INFO @ Wed, 22 Apr 2020 07:50:12: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:50:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:50:12: #2 number of paired peaks: 469 WARNING @ Wed, 22 Apr 2020 07:50:12: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Wed, 22 Apr 2020 07:50:12: start model_add_line... INFO @ Wed, 22 Apr 2020 07:50:12: start X-correlation... INFO @ Wed, 22 Apr 2020 07:50:12: end of X-cor INFO @ Wed, 22 Apr 2020 07:50:12: #2 finished! INFO @ Wed, 22 Apr 2020 07:50:12: #2 predicted fragment length is 81 bps INFO @ Wed, 22 Apr 2020 07:50:12: #2 alternative fragment length(s) may be 2,81,126,167,227,247,279,283,305,370,410,474,494,525,547,571 bps INFO @ Wed, 22 Apr 2020 07:50:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.10_model.r WARNING @ Wed, 22 Apr 2020 07:50:12: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:50:12: #2 You may need to consider one of the other alternative d(s): 2,81,126,167,227,247,279,283,305,370,410,474,494,525,547,571 WARNING @ Wed, 22 Apr 2020 07:50:12: #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 07:50:12: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:50:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:50:13: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:50:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:50:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:50:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.10_summits.bed INFO @ Wed, 22 Apr 2020 07:50:13: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (20 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 07:50:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.bam'] # control file = None # effective genome size = 1.21e+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, 22 Apr 2020 07:50:41: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:50:41: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:50:42: #1 tag size is determined as 69 bps INFO @ Wed, 22 Apr 2020 07:50:42: #1 tag size = 69 INFO @ Wed, 22 Apr 2020 07:50:42: #1 total tags in treatment: 212220 INFO @ Wed, 22 Apr 2020 07:50:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:50:42: #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 07:50:42: #1 tags after filtering in treatment: 212220 INFO @ Wed, 22 Apr 2020 07:50:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:50:42: #1 finished! INFO @ Wed, 22 Apr 2020 07:50:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:50:42: #2 number of paired peaks: 469 WARNING @ Wed, 22 Apr 2020 07:50:42: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Wed, 22 Apr 2020 07:50:42: start model_add_line... INFO @ Wed, 22 Apr 2020 07:50:42: start X-correlation... INFO @ Wed, 22 Apr 2020 07:50:42: end of X-cor INFO @ Wed, 22 Apr 2020 07:50:42: #2 finished! INFO @ Wed, 22 Apr 2020 07:50:42: #2 predicted fragment length is 81 bps INFO @ Wed, 22 Apr 2020 07:50:42: #2 alternative fragment length(s) may be 2,81,126,167,227,247,279,283,305,370,410,474,494,525,547,571 bps INFO @ Wed, 22 Apr 2020 07:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.20_model.r WARNING @ Wed, 22 Apr 2020 07:50:42: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:50:42: #2 You may need to consider one of the other alternative d(s): 2,81,126,167,227,247,279,283,305,370,410,474,494,525,547,571 WARNING @ Wed, 22 Apr 2020 07:50:42: #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 07:50:42: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:50:43: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2858297/ERX2858297.20_summits.bed INFO @ Wed, 22 Apr 2020 07:50:43: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling