Job ID = 5720873 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:38:56 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 ) 2020-04-15T17:38:56 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 ) 2020-04-15T17:47:16 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 ) 2020-04-15T17:50:23 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 : 43,555,250 reads read : 43,555,250 reads written : 43,555,250 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:45 43555250 reads; of these: 43555250 (100.00%) were unpaired; of these: 1739561 (3.99%) aligned 0 times 30615047 (70.29%) aligned exactly 1 time 11200642 (25.72%) aligned >1 times 96.01% overall alignment rate Time searching: 00:12:46 Overall time: 00:12:46 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] 6735685 / 41815689 = 0.1611 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 03:16:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.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 03:16:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:16:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:16:20: 1000000 INFO @ Thu, 16 Apr 2020 03:16:25: 2000000 INFO @ Thu, 16 Apr 2020 03:16:31: 3000000 INFO @ Thu, 16 Apr 2020 03:16:36: 4000000 INFO @ Thu, 16 Apr 2020 03:16:41: 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 03:16:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.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 03:16:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:16:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:16:47: 6000000 INFO @ Thu, 16 Apr 2020 03:16:49: 1000000 INFO @ Thu, 16 Apr 2020 03:16:53: 7000000 INFO @ Thu, 16 Apr 2020 03:16:55: 2000000 INFO @ Thu, 16 Apr 2020 03:16:58: 8000000 INFO @ Thu, 16 Apr 2020 03:17:01: 3000000 INFO @ Thu, 16 Apr 2020 03:17:04: 9000000 INFO @ Thu, 16 Apr 2020 03:17:07: 4000000 INFO @ Thu, 16 Apr 2020 03:17:10: 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 03:17:13: 5000000 INFO @ Thu, 16 Apr 2020 03:17:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.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 03:17:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:17:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:17:16: 11000000 INFO @ Thu, 16 Apr 2020 03:17:19: 6000000 INFO @ Thu, 16 Apr 2020 03:17:20: 1000000 INFO @ Thu, 16 Apr 2020 03:17:22: 12000000 INFO @ Thu, 16 Apr 2020 03:17:26: 7000000 INFO @ Thu, 16 Apr 2020 03:17:26: 2000000 INFO @ Thu, 16 Apr 2020 03:17:29: 13000000 INFO @ Thu, 16 Apr 2020 03:17:32: 8000000 INFO @ Thu, 16 Apr 2020 03:17:33: 3000000 INFO @ Thu, 16 Apr 2020 03:17:35: 14000000 INFO @ Thu, 16 Apr 2020 03:17:38: 9000000 INFO @ Thu, 16 Apr 2020 03:17:39: 4000000 INFO @ Thu, 16 Apr 2020 03:17:41: 15000000 INFO @ Thu, 16 Apr 2020 03:17:44: 10000000 INFO @ Thu, 16 Apr 2020 03:17:45: 5000000 INFO @ Thu, 16 Apr 2020 03:17:46: 16000000 INFO @ Thu, 16 Apr 2020 03:17:51: 11000000 INFO @ Thu, 16 Apr 2020 03:17:51: 6000000 INFO @ Thu, 16 Apr 2020 03:17:52: 17000000 INFO @ Thu, 16 Apr 2020 03:17:57: 12000000 INFO @ Thu, 16 Apr 2020 03:17:58: 7000000 INFO @ Thu, 16 Apr 2020 03:17:58: 18000000 INFO @ Thu, 16 Apr 2020 03:18:03: 13000000 INFO @ Thu, 16 Apr 2020 03:18:04: 8000000 INFO @ Thu, 16 Apr 2020 03:18:04: 19000000 INFO @ Thu, 16 Apr 2020 03:18:09: 14000000 INFO @ Thu, 16 Apr 2020 03:18:10: 20000000 INFO @ Thu, 16 Apr 2020 03:18:10: 9000000 INFO @ Thu, 16 Apr 2020 03:18:15: 15000000 INFO @ Thu, 16 Apr 2020 03:18:16: 21000000 INFO @ Thu, 16 Apr 2020 03:18:16: 10000000 INFO @ Thu, 16 Apr 2020 03:18:21: 16000000 INFO @ Thu, 16 Apr 2020 03:18:21: 22000000 INFO @ Thu, 16 Apr 2020 03:18:22: 11000000 INFO @ Thu, 16 Apr 2020 03:18:27: 23000000 INFO @ Thu, 16 Apr 2020 03:18:27: 17000000 INFO @ Thu, 16 Apr 2020 03:18:28: 12000000 INFO @ Thu, 16 Apr 2020 03:18:33: 24000000 INFO @ Thu, 16 Apr 2020 03:18:33: 18000000 INFO @ Thu, 16 Apr 2020 03:18:34: 13000000 INFO @ Thu, 16 Apr 2020 03:18:38: 25000000 INFO @ Thu, 16 Apr 2020 03:18:39: 19000000 INFO @ Thu, 16 Apr 2020 03:18:40: 14000000 INFO @ Thu, 16 Apr 2020 03:18:44: 26000000 INFO @ Thu, 16 Apr 2020 03:18:45: 20000000 INFO @ Thu, 16 Apr 2020 03:18:46: 15000000 INFO @ Thu, 16 Apr 2020 03:18:50: 27000000 INFO @ Thu, 16 Apr 2020 03:18:50: 21000000 INFO @ Thu, 16 Apr 2020 03:18:52: 16000000 INFO @ Thu, 16 Apr 2020 03:18:55: 28000000 INFO @ Thu, 16 Apr 2020 03:18:56: 22000000 INFO @ Thu, 16 Apr 2020 03:18:58: 17000000 INFO @ Thu, 16 Apr 2020 03:19:01: 29000000 INFO @ Thu, 16 Apr 2020 03:19:02: 23000000 INFO @ Thu, 16 Apr 2020 03:19:03: 18000000 INFO @ Thu, 16 Apr 2020 03:19:07: 30000000 INFO @ Thu, 16 Apr 2020 03:19:08: 24000000 INFO @ Thu, 16 Apr 2020 03:19:09: 19000000 INFO @ Thu, 16 Apr 2020 03:19:13: 31000000 INFO @ Thu, 16 Apr 2020 03:19:14: 25000000 INFO @ Thu, 16 Apr 2020 03:19:15: 20000000 INFO @ Thu, 16 Apr 2020 03:19:18: 32000000 INFO @ Thu, 16 Apr 2020 03:19:20: 26000000 INFO @ Thu, 16 Apr 2020 03:19:21: 21000000 INFO @ Thu, 16 Apr 2020 03:19:24: 33000000 INFO @ Thu, 16 Apr 2020 03:19:26: 27000000 INFO @ Thu, 16 Apr 2020 03:19:27: 22000000 INFO @ Thu, 16 Apr 2020 03:19:30: 34000000 INFO @ Thu, 16 Apr 2020 03:19:31: 28000000 INFO @ Thu, 16 Apr 2020 03:19:33: 23000000 INFO @ Thu, 16 Apr 2020 03:19:36: 35000000 INFO @ Thu, 16 Apr 2020 03:19:37: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:19:37: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:19:37: #1 total tags in treatment: 35080004 INFO @ Thu, 16 Apr 2020 03:19:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:19:37: #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 03:19:37: #1 tags after filtering in treatment: 35080004 INFO @ Thu, 16 Apr 2020 03:19:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:19:37: #1 finished! INFO @ Thu, 16 Apr 2020 03:19:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:19:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:19:37: 29000000 INFO @ Thu, 16 Apr 2020 03:19:39: 24000000 INFO @ Thu, 16 Apr 2020 03:19:39: #2 number of paired peaks: 211 WARNING @ Thu, 16 Apr 2020 03:19:39: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Thu, 16 Apr 2020 03:19:39: start model_add_line... INFO @ Thu, 16 Apr 2020 03:19:40: start X-correlation... INFO @ Thu, 16 Apr 2020 03:19:40: end of X-cor INFO @ Thu, 16 Apr 2020 03:19:40: #2 finished! INFO @ Thu, 16 Apr 2020 03:19:40: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 03:19:40: #2 alternative fragment length(s) may be 1,27 bps INFO @ Thu, 16 Apr 2020 03:19:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.05_model.r WARNING @ Thu, 16 Apr 2020 03:19:40: #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 03:19:40: #2 You may need to consider one of the other alternative d(s): 1,27 WARNING @ Thu, 16 Apr 2020 03:19:40: #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 03:19:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:19:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:19:43: 30000000 INFO @ Thu, 16 Apr 2020 03:19:44: 25000000 INFO @ Thu, 16 Apr 2020 03:19:49: 31000000 INFO @ Thu, 16 Apr 2020 03:19:50: 26000000 INFO @ Thu, 16 Apr 2020 03:19:55: 32000000 INFO @ Thu, 16 Apr 2020 03:19:56: 27000000 INFO @ Thu, 16 Apr 2020 03:20:01: 33000000 INFO @ Thu, 16 Apr 2020 03:20:01: 28000000 INFO @ Thu, 16 Apr 2020 03:20:06: 34000000 INFO @ Thu, 16 Apr 2020 03:20:07: 29000000 INFO @ Thu, 16 Apr 2020 03:20:12: 35000000 INFO @ Thu, 16 Apr 2020 03:20:13: 30000000 INFO @ Thu, 16 Apr 2020 03:20:13: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:20:13: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:20:13: #1 total tags in treatment: 35080004 INFO @ Thu, 16 Apr 2020 03:20:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:20:13: #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 03:20:13: #1 tags after filtering in treatment: 35080004 INFO @ Thu, 16 Apr 2020 03:20:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:20:13: #1 finished! INFO @ Thu, 16 Apr 2020 03:20:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:20:16: #2 number of paired peaks: 211 WARNING @ Thu, 16 Apr 2020 03:20:16: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Thu, 16 Apr 2020 03:20:16: start model_add_line... INFO @ Thu, 16 Apr 2020 03:20:16: start X-correlation... INFO @ Thu, 16 Apr 2020 03:20:16: end of X-cor INFO @ Thu, 16 Apr 2020 03:20:16: #2 finished! INFO @ Thu, 16 Apr 2020 03:20:16: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 03:20:16: #2 alternative fragment length(s) may be 1,27 bps INFO @ Thu, 16 Apr 2020 03:20:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.10_model.r WARNING @ Thu, 16 Apr 2020 03:20:16: #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 03:20:16: #2 You may need to consider one of the other alternative d(s): 1,27 WARNING @ Thu, 16 Apr 2020 03:20:16: #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 03:20:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:20:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:20:18: 31000000 INFO @ Thu, 16 Apr 2020 03:20:24: 32000000 INFO @ Thu, 16 Apr 2020 03:20:29: 33000000 INFO @ Thu, 16 Apr 2020 03:20:32: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:20:35: 34000000 INFO @ Thu, 16 Apr 2020 03:20:40: 35000000 INFO @ Thu, 16 Apr 2020 03:20:41: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:20:41: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:20:41: #1 total tags in treatment: 35080004 INFO @ Thu, 16 Apr 2020 03:20:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:20:41: #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 03:20:41: #1 tags after filtering in treatment: 35080004 INFO @ Thu, 16 Apr 2020 03:20:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:20:41: #1 finished! INFO @ Thu, 16 Apr 2020 03:20:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:20:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:20:43: #2 number of paired peaks: 211 WARNING @ Thu, 16 Apr 2020 03:20:43: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Thu, 16 Apr 2020 03:20:43: start model_add_line... INFO @ Thu, 16 Apr 2020 03:20:44: start X-correlation... INFO @ Thu, 16 Apr 2020 03:20:44: end of X-cor INFO @ Thu, 16 Apr 2020 03:20:44: #2 finished! INFO @ Thu, 16 Apr 2020 03:20:44: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 03:20:44: #2 alternative fragment length(s) may be 1,27 bps INFO @ Thu, 16 Apr 2020 03:20:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.20_model.r WARNING @ Thu, 16 Apr 2020 03:20:44: #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 03:20:44: #2 You may need to consider one of the other alternative d(s): 1,27 WARNING @ Thu, 16 Apr 2020 03:20:44: #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 03:20:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:20:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:20:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:20:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:20:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.05_summits.bed INFO @ Thu, 16 Apr 2020 03:20:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:21:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:21:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:21:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:21:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.10_summits.bed INFO @ Thu, 16 Apr 2020 03:21:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:21:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:21:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:21:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:21:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436059/SRX5436059.20_summits.bed INFO @ Thu, 16 Apr 2020 03:21:59: 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。