Job ID = 5720835 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T16:49:30 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 : 50,454,880 reads read : 50,454,880 reads written : 50,454,880 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: 00:26:35 50454880 reads; of these: 50454880 (100.00%) were unpaired; of these: 3714871 (7.36%) aligned 0 times 24211227 (47.99%) aligned exactly 1 time 22528782 (44.65%) aligned >1 times 92.64% overall alignment rate Time searching: 00:26:35 Overall time: 00:26:35 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 20 files... [bam_rmdupse_core] 23630634 / 46740009 = 0.5056 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 02:49:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.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 02:49:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:49:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:49:09: 1000000 INFO @ Thu, 16 Apr 2020 02:49:14: 2000000 INFO @ Thu, 16 Apr 2020 02:49:19: 3000000 INFO @ Thu, 16 Apr 2020 02:49:24: 4000000 INFO @ Thu, 16 Apr 2020 02:49:29: 5000000 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 02:49:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.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 02:49:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:49:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:49:34: 6000000 INFO @ Thu, 16 Apr 2020 02:49:40: 1000000 INFO @ Thu, 16 Apr 2020 02:49:40: 7000000 INFO @ Thu, 16 Apr 2020 02:49:45: 2000000 INFO @ Thu, 16 Apr 2020 02:49:45: 8000000 INFO @ Thu, 16 Apr 2020 02:49:51: 3000000 INFO @ Thu, 16 Apr 2020 02:49:51: 9000000 INFO @ Thu, 16 Apr 2020 02:49:56: 4000000 INFO @ Thu, 16 Apr 2020 02:49:57: 10000000 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 02:50:02: 5000000 INFO @ Thu, 16 Apr 2020 02:50:02: 11000000 INFO @ Thu, 16 Apr 2020 02:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.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 02:50:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:50:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:50:08: 6000000 INFO @ Thu, 16 Apr 2020 02:50:08: 12000000 INFO @ Thu, 16 Apr 2020 02:50:10: 1000000 INFO @ Thu, 16 Apr 2020 02:50:13: 7000000 INFO @ Thu, 16 Apr 2020 02:50:13: 13000000 INFO @ Thu, 16 Apr 2020 02:50:16: 2000000 INFO @ Thu, 16 Apr 2020 02:50:19: 8000000 INFO @ Thu, 16 Apr 2020 02:50:19: 14000000 INFO @ Thu, 16 Apr 2020 02:50:22: 3000000 INFO @ Thu, 16 Apr 2020 02:50:24: 9000000 INFO @ Thu, 16 Apr 2020 02:50:25: 15000000 INFO @ Thu, 16 Apr 2020 02:50:27: 4000000 INFO @ Thu, 16 Apr 2020 02:50:30: 10000000 INFO @ Thu, 16 Apr 2020 02:50:30: 16000000 INFO @ Thu, 16 Apr 2020 02:50:33: 5000000 INFO @ Thu, 16 Apr 2020 02:50:36: 11000000 INFO @ Thu, 16 Apr 2020 02:50:36: 17000000 INFO @ Thu, 16 Apr 2020 02:50:39: 6000000 INFO @ Thu, 16 Apr 2020 02:50:41: 12000000 INFO @ Thu, 16 Apr 2020 02:50:41: 18000000 INFO @ Thu, 16 Apr 2020 02:50:44: 7000000 INFO @ Thu, 16 Apr 2020 02:50:47: 13000000 INFO @ Thu, 16 Apr 2020 02:50:47: 19000000 INFO @ Thu, 16 Apr 2020 02:50:50: 8000000 INFO @ Thu, 16 Apr 2020 02:50:52: 14000000 INFO @ Thu, 16 Apr 2020 02:50:53: 20000000 INFO @ Thu, 16 Apr 2020 02:50:56: 9000000 INFO @ Thu, 16 Apr 2020 02:50:58: 15000000 INFO @ Thu, 16 Apr 2020 02:50:58: 21000000 INFO @ Thu, 16 Apr 2020 02:51:01: 10000000 INFO @ Thu, 16 Apr 2020 02:51:04: 16000000 INFO @ Thu, 16 Apr 2020 02:51:04: 22000000 INFO @ Thu, 16 Apr 2020 02:51:07: 11000000 INFO @ Thu, 16 Apr 2020 02:51:09: 17000000 INFO @ Thu, 16 Apr 2020 02:51:10: 23000000 INFO @ Thu, 16 Apr 2020 02:51:10: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:51:10: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:51:10: #1 total tags in treatment: 23109375 INFO @ Thu, 16 Apr 2020 02:51:10: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:51:10: #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 02:51:11: #1 tags after filtering in treatment: 23109375 INFO @ Thu, 16 Apr 2020 02:51:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:51:11: #1 finished! INFO @ Thu, 16 Apr 2020 02:51:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:51:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:51:12: #2 number of paired peaks: 369 WARNING @ Thu, 16 Apr 2020 02:51:12: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Thu, 16 Apr 2020 02:51:12: start model_add_line... INFO @ Thu, 16 Apr 2020 02:51:12: start X-correlation... INFO @ Thu, 16 Apr 2020 02:51:12: end of X-cor INFO @ Thu, 16 Apr 2020 02:51:12: #2 finished! INFO @ Thu, 16 Apr 2020 02:51:12: #2 predicted fragment length is 56 bps INFO @ Thu, 16 Apr 2020 02:51:12: #2 alternative fragment length(s) may be 56 bps INFO @ Thu, 16 Apr 2020 02:51:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.05_model.r WARNING @ Thu, 16 Apr 2020 02:51:12: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:51:12: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Thu, 16 Apr 2020 02:51:12: #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 02:51:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:51:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:51:12: 12000000 INFO @ Thu, 16 Apr 2020 02:51:15: 18000000 INFO @ Thu, 16 Apr 2020 02:51:18: 13000000 INFO @ Thu, 16 Apr 2020 02:51:21: 19000000 INFO @ Thu, 16 Apr 2020 02:51:24: 14000000 INFO @ Thu, 16 Apr 2020 02:51:26: 20000000 INFO @ Thu, 16 Apr 2020 02:51:29: 15000000 INFO @ Thu, 16 Apr 2020 02:51:32: 21000000 INFO @ Thu, 16 Apr 2020 02:51:35: 16000000 INFO @ Thu, 16 Apr 2020 02:51:38: 22000000 INFO @ Thu, 16 Apr 2020 02:51:41: 17000000 INFO @ Thu, 16 Apr 2020 02:51:43: 23000000 INFO @ Thu, 16 Apr 2020 02:51:44: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:51:44: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:51:44: #1 total tags in treatment: 23109375 INFO @ Thu, 16 Apr 2020 02:51:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:51:44: #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 02:51:44: #1 tags after filtering in treatment: 23109375 INFO @ Thu, 16 Apr 2020 02:51:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:51:44: #1 finished! INFO @ Thu, 16 Apr 2020 02:51:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:51:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:51:46: #2 number of paired peaks: 369 WARNING @ Thu, 16 Apr 2020 02:51:46: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Thu, 16 Apr 2020 02:51:46: start model_add_line... INFO @ Thu, 16 Apr 2020 02:51:46: start X-correlation... INFO @ Thu, 16 Apr 2020 02:51:46: end of X-cor INFO @ Thu, 16 Apr 2020 02:51:46: #2 finished! INFO @ Thu, 16 Apr 2020 02:51:46: #2 predicted fragment length is 56 bps INFO @ Thu, 16 Apr 2020 02:51:46: #2 alternative fragment length(s) may be 56 bps INFO @ Thu, 16 Apr 2020 02:51:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.10_model.r WARNING @ Thu, 16 Apr 2020 02:51:46: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:51:46: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Thu, 16 Apr 2020 02:51:46: #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 02:51:46: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:51:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:51:46: 18000000 INFO @ Thu, 16 Apr 2020 02:51:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:51:52: 19000000 INFO @ Thu, 16 Apr 2020 02:51:57: 20000000 INFO @ Thu, 16 Apr 2020 02:52:02: 21000000 INFO @ Thu, 16 Apr 2020 02:52:08: 22000000 INFO @ Thu, 16 Apr 2020 02:52:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:52:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:52:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.05_summits.bed INFO @ Thu, 16 Apr 2020 02:52:10: Done! INFO @ Thu, 16 Apr 2020 02:52:13: 23000000 INFO @ Thu, 16 Apr 2020 02:52:14: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:52:14: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:52:14: #1 total tags in treatment: 23109375 INFO @ Thu, 16 Apr 2020 02:52:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:52:14: #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 02:52:14: #1 tags after filtering in treatment: 23109375 INFO @ Thu, 16 Apr 2020 02:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:52:14: #1 finished! INFO @ Thu, 16 Apr 2020 02:52:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:52:14: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (9915 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:52:15: #2 number of paired peaks: 369 WARNING @ Thu, 16 Apr 2020 02:52:15: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Thu, 16 Apr 2020 02:52:15: start model_add_line... INFO @ Thu, 16 Apr 2020 02:52:16: start X-correlation... INFO @ Thu, 16 Apr 2020 02:52:16: end of X-cor INFO @ Thu, 16 Apr 2020 02:52:16: #2 finished! INFO @ Thu, 16 Apr 2020 02:52:16: #2 predicted fragment length is 56 bps INFO @ Thu, 16 Apr 2020 02:52:16: #2 alternative fragment length(s) may be 56 bps INFO @ Thu, 16 Apr 2020 02:52:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.20_model.r WARNING @ Thu, 16 Apr 2020 02:52:16: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:52:16: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Thu, 16 Apr 2020 02:52:16: #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 02:52:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:52:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:52:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.10_summits.bed INFO @ Thu, 16 Apr 2020 02:52:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4905 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:52:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:53:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:53:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:53:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5416210/SRX5416210.20_summits.bed INFO @ Thu, 16 Apr 2020 02:53:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2117 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。