Job ID = 5721043 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:54:52 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 ) 2020-04-15T18:54:52 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 ) 2020-04-15T18:54:52 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 ) spots read : 53,730,154 reads read : 53,730,154 reads written : 53,730,154 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: 00:13:31 53730154 reads; of these: 53730154 (100.00%) were unpaired; of these: 19502326 (36.30%) aligned 0 times 24020577 (44.71%) aligned exactly 1 time 10207251 (19.00%) aligned >1 times 63.70% overall alignment rate Time searching: 00:13:31 Overall time: 00:13:31 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 16 files... [bam_rmdupse_core] 18553761 / 34227828 = 0.5421 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 04:27:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.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 04:27:37: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:27:37: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:27:42: 1000000 INFO @ Thu, 16 Apr 2020 04:27:48: 2000000 INFO @ Thu, 16 Apr 2020 04:27:54: 3000000 INFO @ Thu, 16 Apr 2020 04:28:00: 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 04:28:05: 5000000 INFO @ Thu, 16 Apr 2020 04:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.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 04:28:07: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:28:07: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:28:12: 6000000 INFO @ Thu, 16 Apr 2020 04:28:14: 1000000 INFO @ Thu, 16 Apr 2020 04:28:19: 7000000 INFO @ Thu, 16 Apr 2020 04:28:21: 2000000 INFO @ Thu, 16 Apr 2020 04:28:26: 8000000 INFO @ Thu, 16 Apr 2020 04:28:28: 3000000 INFO @ Thu, 16 Apr 2020 04:28:33: 9000000 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 04:28:35: 4000000 INFO @ Thu, 16 Apr 2020 04:28:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.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 04:28:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:28:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:28:40: 10000000 INFO @ Thu, 16 Apr 2020 04:28:42: 5000000 INFO @ Thu, 16 Apr 2020 04:28:44: 1000000 INFO @ Thu, 16 Apr 2020 04:28:48: 11000000 INFO @ Thu, 16 Apr 2020 04:28:50: 6000000 INFO @ Thu, 16 Apr 2020 04:28:52: 2000000 INFO @ Thu, 16 Apr 2020 04:28:55: 12000000 INFO @ Thu, 16 Apr 2020 04:28:57: 7000000 INFO @ Thu, 16 Apr 2020 04:29:01: 3000000 INFO @ Thu, 16 Apr 2020 04:29:03: 13000000 INFO @ Thu, 16 Apr 2020 04:29:05: 8000000 INFO @ Thu, 16 Apr 2020 04:29:09: 4000000 INFO @ Thu, 16 Apr 2020 04:29:10: 14000000 INFO @ Thu, 16 Apr 2020 04:29:12: 9000000 INFO @ Thu, 16 Apr 2020 04:29:17: 5000000 INFO @ Thu, 16 Apr 2020 04:29:18: 15000000 INFO @ Thu, 16 Apr 2020 04:29:20: 10000000 INFO @ Thu, 16 Apr 2020 04:29:23: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 04:29:23: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 04:29:23: #1 total tags in treatment: 15674067 INFO @ Thu, 16 Apr 2020 04:29:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:29:23: #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 04:29:23: #1 tags after filtering in treatment: 15674067 INFO @ Thu, 16 Apr 2020 04:29:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 04:29:23: #1 finished! INFO @ Thu, 16 Apr 2020 04:29:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:29:24: #2 number of paired peaks: 166 WARNING @ Thu, 16 Apr 2020 04:29:24: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Thu, 16 Apr 2020 04:29:24: start model_add_line... INFO @ Thu, 16 Apr 2020 04:29:24: start X-correlation... INFO @ Thu, 16 Apr 2020 04:29:24: end of X-cor INFO @ Thu, 16 Apr 2020 04:29:24: #2 finished! INFO @ Thu, 16 Apr 2020 04:29:24: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 04:29:24: #2 alternative fragment length(s) may be 51 bps INFO @ Thu, 16 Apr 2020 04:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.05_model.r WARNING @ Thu, 16 Apr 2020 04:29:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:29:24: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Thu, 16 Apr 2020 04:29:24: #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 04:29:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:29:25: 6000000 INFO @ Thu, 16 Apr 2020 04:29:27: 11000000 INFO @ Thu, 16 Apr 2020 04:29:33: 7000000 INFO @ Thu, 16 Apr 2020 04:29:35: 12000000 INFO @ Thu, 16 Apr 2020 04:29:41: 8000000 INFO @ Thu, 16 Apr 2020 04:29:42: 13000000 INFO @ Thu, 16 Apr 2020 04:29:49: 9000000 INFO @ Thu, 16 Apr 2020 04:29:50: 14000000 INFO @ Thu, 16 Apr 2020 04:29:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:29:57: 10000000 INFO @ Thu, 16 Apr 2020 04:29:57: 15000000 INFO @ Thu, 16 Apr 2020 04:30:02: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 04:30:02: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 04:30:02: #1 total tags in treatment: 15674067 INFO @ Thu, 16 Apr 2020 04:30:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:30:02: #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 04:30:02: #1 tags after filtering in treatment: 15674067 INFO @ Thu, 16 Apr 2020 04:30:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 04:30:02: #1 finished! INFO @ Thu, 16 Apr 2020 04:30:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:30:03: #2 number of paired peaks: 166 WARNING @ Thu, 16 Apr 2020 04:30:03: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Thu, 16 Apr 2020 04:30:03: start model_add_line... INFO @ Thu, 16 Apr 2020 04:30:03: start X-correlation... INFO @ Thu, 16 Apr 2020 04:30:03: end of X-cor INFO @ Thu, 16 Apr 2020 04:30:03: #2 finished! INFO @ Thu, 16 Apr 2020 04:30:03: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 04:30:03: #2 alternative fragment length(s) may be 51 bps INFO @ Thu, 16 Apr 2020 04:30:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.10_model.r WARNING @ Thu, 16 Apr 2020 04:30:03: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:30:03: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Thu, 16 Apr 2020 04:30:03: #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 04:30:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:30:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:30:05: 11000000 INFO @ Thu, 16 Apr 2020 04:30:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:30:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:30:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.05_summits.bed INFO @ Thu, 16 Apr 2020 04:30:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2581 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:30:12: 12000000 INFO @ Thu, 16 Apr 2020 04:30:19: 13000000 INFO @ Thu, 16 Apr 2020 04:30:26: 14000000 INFO @ Thu, 16 Apr 2020 04:30:33: 15000000 INFO @ Thu, 16 Apr 2020 04:30:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:30:38: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 04:30:38: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 04:30:38: #1 total tags in treatment: 15674067 INFO @ Thu, 16 Apr 2020 04:30:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:30:38: #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 04:30:38: #1 tags after filtering in treatment: 15674067 INFO @ Thu, 16 Apr 2020 04:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 04:30:38: #1 finished! INFO @ Thu, 16 Apr 2020 04:30:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:30:39: #2 number of paired peaks: 166 WARNING @ Thu, 16 Apr 2020 04:30:39: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Thu, 16 Apr 2020 04:30:39: start model_add_line... INFO @ Thu, 16 Apr 2020 04:30:39: start X-correlation... INFO @ Thu, 16 Apr 2020 04:30:39: end of X-cor INFO @ Thu, 16 Apr 2020 04:30:39: #2 finished! INFO @ Thu, 16 Apr 2020 04:30:39: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 04:30:39: #2 alternative fragment length(s) may be 51 bps INFO @ Thu, 16 Apr 2020 04:30:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.20_model.r WARNING @ Thu, 16 Apr 2020 04:30:39: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:30:39: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Thu, 16 Apr 2020 04:30:39: #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 04:30:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:30:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:30:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:30:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:30:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.10_summits.bed INFO @ Thu, 16 Apr 2020 04:30:50: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1409 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:31:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:31:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:31:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:31:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386777/SRX6386777.20_summits.bed INFO @ Thu, 16 Apr 2020 04:31:23: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (918 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。