Job ID = 5720847 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:12:02 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 ) 2020-04-15T17:20:16 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 ) 2020-04-15T17:20:16 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 ) 2020-04-15T17:20:16 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 ) 2020-04-15T17:20:16 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 ) spots read : 36,010,157 reads read : 36,010,157 reads written : 36,010,157 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: 00:11:32 36010157 reads; of these: 36010157 (100.00%) were unpaired; of these: 1152911 (3.20%) aligned 0 times 23235882 (64.53%) aligned exactly 1 time 11621364 (32.27%) aligned >1 times 96.80% overall alignment rate Time searching: 00:11:32 Overall time: 00:11:32 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] 5877616 / 34857246 = 0.1686 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 02:43:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.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 02:43:45: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:43:45: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:43:53: 1000000 INFO @ Thu, 16 Apr 2020 02:44:00: 2000000 INFO @ Thu, 16 Apr 2020 02:44:08: 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 02:44:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.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 02:44:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:44:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:44:15: 4000000 INFO @ Thu, 16 Apr 2020 02:44:22: 1000000 INFO @ Thu, 16 Apr 2020 02:44:23: 5000000 INFO @ Thu, 16 Apr 2020 02:44:30: 6000000 INFO @ Thu, 16 Apr 2020 02:44:31: 2000000 INFO @ Thu, 16 Apr 2020 02:44:39: 7000000 INFO @ Thu, 16 Apr 2020 02:44:40: 3000000 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 02:44:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.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 02:44:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:44:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:44:48: 8000000 INFO @ Thu, 16 Apr 2020 02:44:48: 4000000 INFO @ Thu, 16 Apr 2020 02:44:53: 1000000 INFO @ Thu, 16 Apr 2020 02:44:56: 9000000 INFO @ Thu, 16 Apr 2020 02:44:56: 5000000 INFO @ Thu, 16 Apr 2020 02:45:00: 2000000 INFO @ Thu, 16 Apr 2020 02:45:04: 10000000 INFO @ Thu, 16 Apr 2020 02:45:04: 6000000 INFO @ Thu, 16 Apr 2020 02:45:08: 3000000 INFO @ Thu, 16 Apr 2020 02:45:12: 11000000 INFO @ Thu, 16 Apr 2020 02:45:12: 7000000 INFO @ Thu, 16 Apr 2020 02:45:16: 4000000 INFO @ Thu, 16 Apr 2020 02:45:19: 12000000 INFO @ Thu, 16 Apr 2020 02:45:19: 8000000 INFO @ Thu, 16 Apr 2020 02:45:25: 5000000 INFO @ Thu, 16 Apr 2020 02:45:26: 13000000 INFO @ Thu, 16 Apr 2020 02:45:28: 9000000 INFO @ Thu, 16 Apr 2020 02:45:33: 6000000 INFO @ Thu, 16 Apr 2020 02:45:34: 14000000 INFO @ Thu, 16 Apr 2020 02:45:35: 10000000 INFO @ Thu, 16 Apr 2020 02:45:41: 15000000 INFO @ Thu, 16 Apr 2020 02:45:41: 7000000 INFO @ Thu, 16 Apr 2020 02:45:44: 11000000 INFO @ Thu, 16 Apr 2020 02:45:49: 16000000 INFO @ Thu, 16 Apr 2020 02:45:49: 8000000 INFO @ Thu, 16 Apr 2020 02:45:52: 12000000 INFO @ Thu, 16 Apr 2020 02:45:56: 17000000 INFO @ Thu, 16 Apr 2020 02:45:57: 9000000 INFO @ Thu, 16 Apr 2020 02:46:01: 13000000 INFO @ Thu, 16 Apr 2020 02:46:04: 18000000 INFO @ Thu, 16 Apr 2020 02:46:07: 10000000 INFO @ Thu, 16 Apr 2020 02:46:10: 14000000 INFO @ Thu, 16 Apr 2020 02:46:12: 19000000 INFO @ Thu, 16 Apr 2020 02:46:15: 11000000 INFO @ Thu, 16 Apr 2020 02:46:18: 15000000 INFO @ Thu, 16 Apr 2020 02:46:20: 20000000 INFO @ Thu, 16 Apr 2020 02:46:23: 12000000 INFO @ Thu, 16 Apr 2020 02:46:27: 16000000 INFO @ Thu, 16 Apr 2020 02:46:30: 21000000 INFO @ Thu, 16 Apr 2020 02:46:32: 13000000 INFO @ Thu, 16 Apr 2020 02:46:34: 17000000 INFO @ Thu, 16 Apr 2020 02:46:39: 22000000 INFO @ Thu, 16 Apr 2020 02:46:42: 18000000 INFO @ Thu, 16 Apr 2020 02:46:44: 14000000 INFO @ Thu, 16 Apr 2020 02:46:48: 23000000 INFO @ Thu, 16 Apr 2020 02:46:50: 19000000 INFO @ Thu, 16 Apr 2020 02:46:53: 15000000 INFO @ Thu, 16 Apr 2020 02:46:55: 24000000 INFO @ Thu, 16 Apr 2020 02:46:58: 20000000 INFO @ Thu, 16 Apr 2020 02:47:00: 16000000 INFO @ Thu, 16 Apr 2020 02:47:05: 25000000 INFO @ Thu, 16 Apr 2020 02:47:08: 21000000 INFO @ Thu, 16 Apr 2020 02:47:08: 17000000 INFO @ Thu, 16 Apr 2020 02:47:14: 26000000 INFO @ Thu, 16 Apr 2020 02:47:17: 22000000 INFO @ Thu, 16 Apr 2020 02:47:17: 18000000 INFO @ Thu, 16 Apr 2020 02:47:22: 27000000 INFO @ Thu, 16 Apr 2020 02:47:24: 23000000 INFO @ Thu, 16 Apr 2020 02:47:27: 19000000 INFO @ Thu, 16 Apr 2020 02:47:30: 28000000 INFO @ Thu, 16 Apr 2020 02:47:31: 24000000 INFO @ Thu, 16 Apr 2020 02:47:35: 20000000 INFO @ Thu, 16 Apr 2020 02:47:39: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:47:39: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:47:39: #1 total tags in treatment: 28979630 INFO @ Thu, 16 Apr 2020 02:47:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:47:39: #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 02:47:39: 25000000 INFO @ Thu, 16 Apr 2020 02:47:39: #1 tags after filtering in treatment: 28979630 INFO @ Thu, 16 Apr 2020 02:47:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:47:39: #1 finished! INFO @ Thu, 16 Apr 2020 02:47:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:47:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:47:42: #2 number of paired peaks: 422 WARNING @ Thu, 16 Apr 2020 02:47:42: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Thu, 16 Apr 2020 02:47:42: start model_add_line... INFO @ Thu, 16 Apr 2020 02:47:42: start X-correlation... INFO @ Thu, 16 Apr 2020 02:47:42: end of X-cor INFO @ Thu, 16 Apr 2020 02:47:42: #2 finished! INFO @ Thu, 16 Apr 2020 02:47:42: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:47:42: #2 alternative fragment length(s) may be 1,45,539,566,591 bps INFO @ Thu, 16 Apr 2020 02:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.05_model.r WARNING @ Thu, 16 Apr 2020 02:47:42: #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 02:47:42: #2 You may need to consider one of the other alternative d(s): 1,45,539,566,591 WARNING @ Thu, 16 Apr 2020 02:47:42: #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 02:47:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:47:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:47:44: 21000000 INFO @ Thu, 16 Apr 2020 02:47:47: 26000000 INFO @ Thu, 16 Apr 2020 02:47:51: 22000000 INFO @ Thu, 16 Apr 2020 02:47:55: 27000000 INFO @ Thu, 16 Apr 2020 02:47:59: 23000000 INFO @ Thu, 16 Apr 2020 02:48:03: 28000000 INFO @ Thu, 16 Apr 2020 02:48:08: 24000000 INFO @ Thu, 16 Apr 2020 02:48:11: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:48:11: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:48:11: #1 total tags in treatment: 28979630 INFO @ Thu, 16 Apr 2020 02:48:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:48:11: #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 02:48:12: #1 tags after filtering in treatment: 28979630 INFO @ Thu, 16 Apr 2020 02:48:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:48:12: #1 finished! INFO @ Thu, 16 Apr 2020 02:48:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:48:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:48:15: #2 number of paired peaks: 422 WARNING @ Thu, 16 Apr 2020 02:48:15: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Thu, 16 Apr 2020 02:48:15: start model_add_line... INFO @ Thu, 16 Apr 2020 02:48:15: start X-correlation... INFO @ Thu, 16 Apr 2020 02:48:15: end of X-cor INFO @ Thu, 16 Apr 2020 02:48:15: #2 finished! INFO @ Thu, 16 Apr 2020 02:48:15: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:48:15: #2 alternative fragment length(s) may be 1,45,539,566,591 bps INFO @ Thu, 16 Apr 2020 02:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.10_model.r WARNING @ Thu, 16 Apr 2020 02:48:15: #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 02:48:15: #2 You may need to consider one of the other alternative d(s): 1,45,539,566,591 WARNING @ Thu, 16 Apr 2020 02:48:15: #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 02:48:15: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:48:17: 25000000 INFO @ Thu, 16 Apr 2020 02:48:24: 26000000 INFO @ Thu, 16 Apr 2020 02:48:30: 27000000 INFO @ Thu, 16 Apr 2020 02:48:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:48:36: 28000000 INFO @ Thu, 16 Apr 2020 02:48:42: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:48:42: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:48:42: #1 total tags in treatment: 28979630 INFO @ Thu, 16 Apr 2020 02:48:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:48:42: #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 02:48:42: #1 tags after filtering in treatment: 28979630 INFO @ Thu, 16 Apr 2020 02:48:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:48:42: #1 finished! INFO @ Thu, 16 Apr 2020 02:48:42: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:48:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:48:44: #2 number of paired peaks: 422 WARNING @ Thu, 16 Apr 2020 02:48:44: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Thu, 16 Apr 2020 02:48:44: start model_add_line... INFO @ Thu, 16 Apr 2020 02:48:44: start X-correlation... INFO @ Thu, 16 Apr 2020 02:48:44: end of X-cor INFO @ Thu, 16 Apr 2020 02:48:44: #2 finished! INFO @ Thu, 16 Apr 2020 02:48:44: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:48:44: #2 alternative fragment length(s) may be 1,45,539,566,591 bps INFO @ Thu, 16 Apr 2020 02:48:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.20_model.r WARNING @ Thu, 16 Apr 2020 02:48:44: #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 02:48:44: #2 You may need to consider one of the other alternative d(s): 1,45,539,566,591 WARNING @ Thu, 16 Apr 2020 02:48:44: #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 02:48:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:48:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:48:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:48:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:48:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.05_summits.bed INFO @ Thu, 16 Apr 2020 02:48:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:49:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:49:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:49:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:49:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.10_summits.bed INFO @ Thu, 16 Apr 2020 02:49:21: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:49:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:49:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:49:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:49:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436040/SRX5436040.20_summits.bed INFO @ Thu, 16 Apr 2020 02:49:50: 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。