Job ID = 5721167 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T20:36:20 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 ) 2020-04-15T20:36:20 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 ) 2020-04-15T20:36:21 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 ) 2020-04-15T20:36:21 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 : 27,510,463 reads read : 55,020,926 reads written : 27,510,463 reads 0-length : 27,510,463 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: 00:08:03 27510463 reads; of these: 27510463 (100.00%) were unpaired; of these: 13253487 (48.18%) aligned 0 times 9674176 (35.17%) aligned exactly 1 time 4582800 (16.66%) aligned >1 times 51.82% overall alignment rate Time searching: 00:08:03 Overall time: 00:08:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1988818 / 14256976 = 0.1395 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 05:49:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.bam'] # control file = None # effective genome size = 1.20e+08 # 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 05:49:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:49:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:49:50: 1000000 INFO @ Thu, 16 Apr 2020 05:49:59: 2000000 INFO @ Thu, 16 Apr 2020 05:50:07: 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 05:50:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.bam'] # control file = None # effective genome size = 1.20e+08 # 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 05:50:12: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:50:12: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:50:14: 4000000 INFO @ Thu, 16 Apr 2020 05:50:19: 1000000 INFO @ Thu, 16 Apr 2020 05:50:22: 5000000 INFO @ Thu, 16 Apr 2020 05:50:26: 2000000 INFO @ Thu, 16 Apr 2020 05:50:30: 6000000 INFO @ Thu, 16 Apr 2020 05:50:34: 3000000 INFO @ Thu, 16 Apr 2020 05:50:38: 7000000 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 05:50:41: 4000000 INFO @ Thu, 16 Apr 2020 05:50:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.bam'] # control file = None # effective genome size = 1.20e+08 # 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 05:50:42: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:50:42: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:50:46: 8000000 INFO @ Thu, 16 Apr 2020 05:50:48: 5000000 INFO @ Thu, 16 Apr 2020 05:50:50: 1000000 INFO @ Thu, 16 Apr 2020 05:50:54: 9000000 INFO @ Thu, 16 Apr 2020 05:50:55: 6000000 INFO @ Thu, 16 Apr 2020 05:50:58: 2000000 INFO @ Thu, 16 Apr 2020 05:51:01: 10000000 INFO @ Thu, 16 Apr 2020 05:51:03: 7000000 INFO @ Thu, 16 Apr 2020 05:51:06: 3000000 INFO @ Thu, 16 Apr 2020 05:51:09: 11000000 INFO @ Thu, 16 Apr 2020 05:51:10: 8000000 INFO @ Thu, 16 Apr 2020 05:51:14: 4000000 INFO @ Thu, 16 Apr 2020 05:51:18: 9000000 INFO @ Thu, 16 Apr 2020 05:51:18: 12000000 INFO @ Thu, 16 Apr 2020 05:51:20: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:51:20: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:51:20: #1 total tags in treatment: 12268158 INFO @ Thu, 16 Apr 2020 05:51:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:51:20: #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 05:51:20: #1 tags after filtering in treatment: 12268158 INFO @ Thu, 16 Apr 2020 05:51:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:51:20: #1 finished! INFO @ Thu, 16 Apr 2020 05:51:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:51:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:51:21: #2 number of paired peaks: 966 WARNING @ Thu, 16 Apr 2020 05:51:21: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Thu, 16 Apr 2020 05:51:21: start model_add_line... INFO @ Thu, 16 Apr 2020 05:51:21: start X-correlation... INFO @ Thu, 16 Apr 2020 05:51:21: end of X-cor INFO @ Thu, 16 Apr 2020 05:51:21: #2 finished! INFO @ Thu, 16 Apr 2020 05:51:21: #2 predicted fragment length is 74 bps INFO @ Thu, 16 Apr 2020 05:51:21: #2 alternative fragment length(s) may be 3,74 bps INFO @ Thu, 16 Apr 2020 05:51:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.05_model.r WARNING @ Thu, 16 Apr 2020 05:51:21: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:51:21: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Thu, 16 Apr 2020 05:51:21: #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 05:51:21: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:51:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:51:21: 5000000 INFO @ Thu, 16 Apr 2020 05:51:25: 10000000 INFO @ Thu, 16 Apr 2020 05:51:29: 6000000 INFO @ Thu, 16 Apr 2020 05:51:32: 11000000 INFO @ Thu, 16 Apr 2020 05:51:37: 7000000 INFO @ Thu, 16 Apr 2020 05:51:40: 12000000 INFO @ Thu, 16 Apr 2020 05:51:42: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:51:42: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:51:42: #1 total tags in treatment: 12268158 INFO @ Thu, 16 Apr 2020 05:51:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:51:42: #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 05:51:42: #1 tags after filtering in treatment: 12268158 INFO @ Thu, 16 Apr 2020 05:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:51:42: #1 finished! INFO @ Thu, 16 Apr 2020 05:51:42: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:51:43: #2 number of paired peaks: 966 WARNING @ Thu, 16 Apr 2020 05:51:43: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Thu, 16 Apr 2020 05:51:43: start model_add_line... INFO @ Thu, 16 Apr 2020 05:51:43: start X-correlation... INFO @ Thu, 16 Apr 2020 05:51:43: end of X-cor INFO @ Thu, 16 Apr 2020 05:51:43: #2 finished! INFO @ Thu, 16 Apr 2020 05:51:43: #2 predicted fragment length is 74 bps INFO @ Thu, 16 Apr 2020 05:51:43: #2 alternative fragment length(s) may be 3,74 bps INFO @ Thu, 16 Apr 2020 05:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.10_model.r WARNING @ Thu, 16 Apr 2020 05:51:43: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:51:43: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Thu, 16 Apr 2020 05:51:43: #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 05:51:43: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:51:45: 8000000 INFO @ Thu, 16 Apr 2020 05:51:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:51:52: 9000000 INFO @ Thu, 16 Apr 2020 05:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.05_summits.bed INFO @ Thu, 16 Apr 2020 05:51:57: Done! INFO @ Thu, 16 Apr 2020 05:51:59: 10000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2704 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:52:06: 11000000 INFO @ Thu, 16 Apr 2020 05:52:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:52:14: 12000000 INFO @ Thu, 16 Apr 2020 05:52:15: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:52:15: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:52:15: #1 total tags in treatment: 12268158 INFO @ Thu, 16 Apr 2020 05:52:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:52:15: #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 05:52:16: #1 tags after filtering in treatment: 12268158 INFO @ Thu, 16 Apr 2020 05:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:52:16: #1 finished! INFO @ Thu, 16 Apr 2020 05:52:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:52:17: #2 number of paired peaks: 966 WARNING @ Thu, 16 Apr 2020 05:52:17: Fewer paired peaks (966) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 966 pairs to build model! INFO @ Thu, 16 Apr 2020 05:52:17: start model_add_line... INFO @ Thu, 16 Apr 2020 05:52:17: start X-correlation... INFO @ Thu, 16 Apr 2020 05:52:17: end of X-cor INFO @ Thu, 16 Apr 2020 05:52:17: #2 finished! INFO @ Thu, 16 Apr 2020 05:52:17: #2 predicted fragment length is 74 bps INFO @ Thu, 16 Apr 2020 05:52:17: #2 alternative fragment length(s) may be 3,74 bps INFO @ Thu, 16 Apr 2020 05:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.20_model.r WARNING @ Thu, 16 Apr 2020 05:52:17: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:52:17: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Thu, 16 Apr 2020 05:52:17: #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 05:52:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:52:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:52:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:52:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.10_summits.bed INFO @ Thu, 16 Apr 2020 05:52:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1607 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:52:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:52:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:52:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:52:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6747984/SRX6747984.20_summits.bed INFO @ Thu, 16 Apr 2020 05:52:52: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (758 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。