Job ID = 5720842 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:03:17 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 ) 2020-04-15T17:03:17 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 : 35,422,362 reads read : 35,422,362 reads written : 35,422,362 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: 00:11:16 35422362 reads; of these: 35422362 (100.00%) were unpaired; of these: 1119116 (3.16%) aligned 0 times 23028050 (65.01%) aligned exactly 1 time 11275196 (31.83%) aligned >1 times 96.84% overall alignment rate Time searching: 00:11:16 Overall time: 00:11:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 5713792 / 34303246 = 0.1666 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 02:32:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.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 02:32:29: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:32:29: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:32:34: 1000000 INFO @ Thu, 16 Apr 2020 02:32:39: 2000000 INFO @ Thu, 16 Apr 2020 02:32:43: 3000000 INFO @ Thu, 16 Apr 2020 02:32:48: 4000000 INFO @ Thu, 16 Apr 2020 02:32:53: 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 02:32:58: 6000000 INFO @ Thu, 16 Apr 2020 02:32:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.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 02:32:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:32:59: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:33:03: 7000000 INFO @ Thu, 16 Apr 2020 02:33:04: 1000000 INFO @ Thu, 16 Apr 2020 02:33:08: 8000000 INFO @ Thu, 16 Apr 2020 02:33:09: 2000000 INFO @ Thu, 16 Apr 2020 02:33:13: 9000000 INFO @ Thu, 16 Apr 2020 02:33:15: 3000000 INFO @ Thu, 16 Apr 2020 02:33:18: 10000000 INFO @ Thu, 16 Apr 2020 02:33:20: 4000000 INFO @ Thu, 16 Apr 2020 02:33:23: 11000000 INFO @ Thu, 16 Apr 2020 02:33:25: 5000000 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 02:33:28: 12000000 INFO @ Thu, 16 Apr 2020 02:33:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.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 02:33:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:33:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:33:30: 6000000 INFO @ Thu, 16 Apr 2020 02:33:33: 13000000 INFO @ Thu, 16 Apr 2020 02:33:34: 1000000 INFO @ Thu, 16 Apr 2020 02:33:35: 7000000 INFO @ Thu, 16 Apr 2020 02:33:38: 14000000 INFO @ Thu, 16 Apr 2020 02:33:39: 2000000 INFO @ Thu, 16 Apr 2020 02:33:40: 8000000 INFO @ Thu, 16 Apr 2020 02:33:43: 15000000 INFO @ Thu, 16 Apr 2020 02:33:44: 3000000 INFO @ Thu, 16 Apr 2020 02:33:45: 9000000 INFO @ Thu, 16 Apr 2020 02:33:48: 16000000 INFO @ Thu, 16 Apr 2020 02:33:49: 4000000 INFO @ Thu, 16 Apr 2020 02:33:50: 10000000 INFO @ Thu, 16 Apr 2020 02:33:53: 17000000 INFO @ Thu, 16 Apr 2020 02:33:54: 5000000 INFO @ Thu, 16 Apr 2020 02:33:55: 11000000 INFO @ Thu, 16 Apr 2020 02:33:58: 18000000 INFO @ Thu, 16 Apr 2020 02:33:59: 6000000 INFO @ Thu, 16 Apr 2020 02:34:01: 12000000 INFO @ Thu, 16 Apr 2020 02:34:03: 19000000 INFO @ Thu, 16 Apr 2020 02:34:04: 7000000 INFO @ Thu, 16 Apr 2020 02:34:06: 13000000 INFO @ Thu, 16 Apr 2020 02:34:08: 20000000 INFO @ Thu, 16 Apr 2020 02:34:09: 8000000 INFO @ Thu, 16 Apr 2020 02:34:11: 14000000 INFO @ Thu, 16 Apr 2020 02:34:13: 21000000 INFO @ Thu, 16 Apr 2020 02:34:14: 9000000 INFO @ Thu, 16 Apr 2020 02:34:16: 15000000 INFO @ Thu, 16 Apr 2020 02:34:18: 22000000 INFO @ Thu, 16 Apr 2020 02:34:19: 10000000 INFO @ Thu, 16 Apr 2020 02:34:21: 16000000 INFO @ Thu, 16 Apr 2020 02:34:24: 23000000 INFO @ Thu, 16 Apr 2020 02:34:24: 11000000 INFO @ Thu, 16 Apr 2020 02:34:26: 17000000 INFO @ Thu, 16 Apr 2020 02:34:29: 24000000 INFO @ Thu, 16 Apr 2020 02:34:29: 12000000 INFO @ Thu, 16 Apr 2020 02:34:31: 18000000 INFO @ Thu, 16 Apr 2020 02:34:34: 25000000 INFO @ Thu, 16 Apr 2020 02:34:34: 13000000 INFO @ Thu, 16 Apr 2020 02:34:36: 19000000 INFO @ Thu, 16 Apr 2020 02:34:39: 26000000 INFO @ Thu, 16 Apr 2020 02:34:39: 14000000 INFO @ Thu, 16 Apr 2020 02:34:41: 20000000 INFO @ Thu, 16 Apr 2020 02:34:44: 27000000 INFO @ Thu, 16 Apr 2020 02:34:44: 15000000 INFO @ Thu, 16 Apr 2020 02:34:46: 21000000 INFO @ Thu, 16 Apr 2020 02:34:49: 28000000 INFO @ Thu, 16 Apr 2020 02:34:49: 16000000 INFO @ Thu, 16 Apr 2020 02:34:51: 22000000 INFO @ Thu, 16 Apr 2020 02:34:52: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:34:52: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:34:52: #1 total tags in treatment: 28589454 INFO @ Thu, 16 Apr 2020 02:34:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:34:52: #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 02:34:53: #1 tags after filtering in treatment: 28589454 INFO @ Thu, 16 Apr 2020 02:34:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:34:53: #1 finished! INFO @ Thu, 16 Apr 2020 02:34:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:34:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:34:54: 17000000 INFO @ Thu, 16 Apr 2020 02:34:55: #2 number of paired peaks: 461 WARNING @ Thu, 16 Apr 2020 02:34:55: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Thu, 16 Apr 2020 02:34:55: start model_add_line... INFO @ Thu, 16 Apr 2020 02:34:55: start X-correlation... INFO @ Thu, 16 Apr 2020 02:34:55: end of X-cor INFO @ Thu, 16 Apr 2020 02:34:55: #2 finished! INFO @ Thu, 16 Apr 2020 02:34:55: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:34:55: #2 alternative fragment length(s) may be 1,24,577 bps INFO @ Thu, 16 Apr 2020 02:34:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.05_model.r WARNING @ Thu, 16 Apr 2020 02:34:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:34:55: #2 You may need to consider one of the other alternative d(s): 1,24,577 WARNING @ Thu, 16 Apr 2020 02:34:55: #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 02:34:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:34:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:34:56: 23000000 INFO @ Thu, 16 Apr 2020 02:34:59: 18000000 INFO @ Thu, 16 Apr 2020 02:35:01: 24000000 INFO @ Thu, 16 Apr 2020 02:35:04: 19000000 INFO @ Thu, 16 Apr 2020 02:35:06: 25000000 INFO @ Thu, 16 Apr 2020 02:35:09: 20000000 INFO @ Thu, 16 Apr 2020 02:35:11: 26000000 INFO @ Thu, 16 Apr 2020 02:35:14: 21000000 INFO @ Thu, 16 Apr 2020 02:35:16: 27000000 INFO @ Thu, 16 Apr 2020 02:35:19: 22000000 INFO @ Thu, 16 Apr 2020 02:35:22: 28000000 INFO @ Thu, 16 Apr 2020 02:35:24: 23000000 INFO @ Thu, 16 Apr 2020 02:35:25: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:35:25: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:35:25: #1 total tags in treatment: 28589454 INFO @ Thu, 16 Apr 2020 02:35:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:35:25: #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 02:35:25: #1 tags after filtering in treatment: 28589454 INFO @ Thu, 16 Apr 2020 02:35:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:35:25: #1 finished! INFO @ Thu, 16 Apr 2020 02:35:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:35:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:35:27: #2 number of paired peaks: 461 WARNING @ Thu, 16 Apr 2020 02:35:27: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Thu, 16 Apr 2020 02:35:27: start model_add_line... INFO @ Thu, 16 Apr 2020 02:35:27: start X-correlation... INFO @ Thu, 16 Apr 2020 02:35:27: end of X-cor INFO @ Thu, 16 Apr 2020 02:35:27: #2 finished! INFO @ Thu, 16 Apr 2020 02:35:27: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:35:27: #2 alternative fragment length(s) may be 1,24,577 bps INFO @ Thu, 16 Apr 2020 02:35:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.10_model.r WARNING @ Thu, 16 Apr 2020 02:35:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:35:27: #2 You may need to consider one of the other alternative d(s): 1,24,577 WARNING @ Thu, 16 Apr 2020 02:35:27: #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 02:35:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:35:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:35:29: 24000000 INFO @ Thu, 16 Apr 2020 02:35:34: 25000000 INFO @ Thu, 16 Apr 2020 02:35:39: 26000000 INFO @ Thu, 16 Apr 2020 02:35:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:35:44: 27000000 INFO @ Thu, 16 Apr 2020 02:35:49: 28000000 INFO @ Thu, 16 Apr 2020 02:35:52: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:35:52: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:35:52: #1 total tags in treatment: 28589454 INFO @ Thu, 16 Apr 2020 02:35:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:35:52: #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 02:35:53: #1 tags after filtering in treatment: 28589454 INFO @ Thu, 16 Apr 2020 02:35:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:35:53: #1 finished! INFO @ Thu, 16 Apr 2020 02:35:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:35:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:35:55: #2 number of paired peaks: 461 WARNING @ Thu, 16 Apr 2020 02:35:55: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Thu, 16 Apr 2020 02:35:55: start model_add_line... INFO @ Thu, 16 Apr 2020 02:35:55: start X-correlation... INFO @ Thu, 16 Apr 2020 02:35:55: end of X-cor INFO @ Thu, 16 Apr 2020 02:35:55: #2 finished! INFO @ Thu, 16 Apr 2020 02:35:55: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:35:55: #2 alternative fragment length(s) may be 1,24,577 bps INFO @ Thu, 16 Apr 2020 02:35:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.20_model.r WARNING @ Thu, 16 Apr 2020 02:35:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:35:55: #2 You may need to consider one of the other alternative d(s): 1,24,577 WARNING @ Thu, 16 Apr 2020 02:35:55: #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 02:35:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:35:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:36:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:36:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:36:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.05_summits.bed INFO @ Thu, 16 Apr 2020 02:36:02: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:36:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:36:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:36:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:36:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.10_summits.bed INFO @ Thu, 16 Apr 2020 02:36:35: Done! INFO @ Thu, 16 Apr 2020 02:36:39: #3 Call peaks for each chromosome... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:37:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436035/SRX5436035.20_summits.bed INFO @ Thu, 16 Apr 2020 02:37:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。