Job ID = 5720845 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:06:03 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 ) 2020-04-15T17:06:03 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 ) 2020-04-15T17:06:03 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 ) 2020-04-15T17:07:59 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 ) 2020-04-15T17:08:10 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 ) 2020-04-15T17:08:10 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 ) 2020-04-15T17:11:10 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 ) 2020-04-15T17:16:48 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 : 35,361,423 reads read : 35,361,423 reads written : 35,361,423 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: 00:11:17 35361423 reads; of these: 35361423 (100.00%) were unpaired; of these: 924575 (2.61%) aligned 0 times 23363525 (66.07%) aligned exactly 1 time 11073323 (31.31%) aligned >1 times 97.39% overall alignment rate Time searching: 00:11:17 Overall time: 00:11:17 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] 5569126 / 34436848 = 0.1617 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 02:41:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.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 02:41:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:41:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:41:28: 1000000 INFO @ Thu, 16 Apr 2020 02:41:33: 2000000 INFO @ Thu, 16 Apr 2020 02:41:38: 3000000 INFO @ Thu, 16 Apr 2020 02:41:43: 4000000 INFO @ Thu, 16 Apr 2020 02:41:47: 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 02:41:52: 6000000 INFO @ Thu, 16 Apr 2020 02:41:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.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 02:41:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:41:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:41:57: 7000000 INFO @ Thu, 16 Apr 2020 02:41:58: 1000000 INFO @ Thu, 16 Apr 2020 02:42:02: 8000000 INFO @ Thu, 16 Apr 2020 02:42:03: 2000000 INFO @ Thu, 16 Apr 2020 02:42:07: 9000000 INFO @ Thu, 16 Apr 2020 02:42:08: 3000000 INFO @ Thu, 16 Apr 2020 02:42:12: 10000000 INFO @ Thu, 16 Apr 2020 02:42:13: 4000000 INFO @ Thu, 16 Apr 2020 02:42:16: 11000000 INFO @ Thu, 16 Apr 2020 02:42:18: 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 02:42:22: 12000000 INFO @ Thu, 16 Apr 2020 02:42:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.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 02:42:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:42:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:42:23: 6000000 INFO @ Thu, 16 Apr 2020 02:42:26: 13000000 INFO @ Thu, 16 Apr 2020 02:42:28: 1000000 INFO @ Thu, 16 Apr 2020 02:42:28: 7000000 INFO @ Thu, 16 Apr 2020 02:42:31: 14000000 INFO @ Thu, 16 Apr 2020 02:42:33: 2000000 INFO @ Thu, 16 Apr 2020 02:42:33: 8000000 INFO @ Thu, 16 Apr 2020 02:42:36: 15000000 INFO @ Thu, 16 Apr 2020 02:42:37: 3000000 INFO @ Thu, 16 Apr 2020 02:42:38: 9000000 INFO @ Thu, 16 Apr 2020 02:42:41: 16000000 INFO @ Thu, 16 Apr 2020 02:42:42: 4000000 INFO @ Thu, 16 Apr 2020 02:42:43: 10000000 INFO @ Thu, 16 Apr 2020 02:42:46: 17000000 INFO @ Thu, 16 Apr 2020 02:42:48: 5000000 INFO @ Thu, 16 Apr 2020 02:42:48: 11000000 INFO @ Thu, 16 Apr 2020 02:42:51: 18000000 INFO @ Thu, 16 Apr 2020 02:42:53: 6000000 INFO @ Thu, 16 Apr 2020 02:42:53: 12000000 INFO @ Thu, 16 Apr 2020 02:42:56: 19000000 INFO @ Thu, 16 Apr 2020 02:42:58: 7000000 INFO @ Thu, 16 Apr 2020 02:42:58: 13000000 INFO @ Thu, 16 Apr 2020 02:43:01: 20000000 INFO @ Thu, 16 Apr 2020 02:43:03: 8000000 INFO @ Thu, 16 Apr 2020 02:43:03: 14000000 INFO @ Thu, 16 Apr 2020 02:43:05: 21000000 INFO @ Thu, 16 Apr 2020 02:43:08: 9000000 INFO @ Thu, 16 Apr 2020 02:43:09: 15000000 INFO @ Thu, 16 Apr 2020 02:43:10: 22000000 INFO @ Thu, 16 Apr 2020 02:43:13: 10000000 INFO @ Thu, 16 Apr 2020 02:43:14: 16000000 INFO @ Thu, 16 Apr 2020 02:43:15: 23000000 INFO @ Thu, 16 Apr 2020 02:43:18: 11000000 INFO @ Thu, 16 Apr 2020 02:43:19: 17000000 INFO @ Thu, 16 Apr 2020 02:43:20: 24000000 INFO @ Thu, 16 Apr 2020 02:43:23: 12000000 INFO @ Thu, 16 Apr 2020 02:43:24: 18000000 INFO @ Thu, 16 Apr 2020 02:43:25: 25000000 INFO @ Thu, 16 Apr 2020 02:43:28: 13000000 INFO @ Thu, 16 Apr 2020 02:43:29: 19000000 INFO @ Thu, 16 Apr 2020 02:43:30: 26000000 INFO @ Thu, 16 Apr 2020 02:43:33: 14000000 INFO @ Thu, 16 Apr 2020 02:43:34: 20000000 INFO @ Thu, 16 Apr 2020 02:43:35: 27000000 INFO @ Thu, 16 Apr 2020 02:43:38: 15000000 INFO @ Thu, 16 Apr 2020 02:43:38: 21000000 INFO @ Thu, 16 Apr 2020 02:43:40: 28000000 INFO @ Thu, 16 Apr 2020 02:43:43: 16000000 INFO @ Thu, 16 Apr 2020 02:43:43: 22000000 INFO @ Thu, 16 Apr 2020 02:43:44: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:43:44: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:43:44: #1 total tags in treatment: 28867722 INFO @ Thu, 16 Apr 2020 02:43:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:43:44: #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 02:43:45: #1 tags after filtering in treatment: 28867722 INFO @ Thu, 16 Apr 2020 02:43:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:43:45: #1 finished! INFO @ Thu, 16 Apr 2020 02:43:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:43:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:43:47: #2 number of paired peaks: 465 WARNING @ Thu, 16 Apr 2020 02:43:47: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Thu, 16 Apr 2020 02:43:47: start model_add_line... INFO @ Thu, 16 Apr 2020 02:43:47: start X-correlation... INFO @ Thu, 16 Apr 2020 02:43:47: end of X-cor INFO @ Thu, 16 Apr 2020 02:43:47: #2 finished! INFO @ Thu, 16 Apr 2020 02:43:47: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:43:47: #2 alternative fragment length(s) may be 1,16,29 bps INFO @ Thu, 16 Apr 2020 02:43:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.05_model.r WARNING @ Thu, 16 Apr 2020 02:43:47: #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 02:43:47: #2 You may need to consider one of the other alternative d(s): 1,16,29 WARNING @ Thu, 16 Apr 2020 02:43:47: #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 02:43:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:43:48: 17000000 INFO @ Thu, 16 Apr 2020 02:43:48: 23000000 INFO @ Thu, 16 Apr 2020 02:43:53: 18000000 INFO @ Thu, 16 Apr 2020 02:43:53: 24000000 INFO @ Thu, 16 Apr 2020 02:43:58: 19000000 INFO @ Thu, 16 Apr 2020 02:43:58: 25000000 INFO @ Thu, 16 Apr 2020 02:44:03: 20000000 INFO @ Thu, 16 Apr 2020 02:44:03: 26000000 INFO @ Thu, 16 Apr 2020 02:44:08: 21000000 INFO @ Thu, 16 Apr 2020 02:44:08: 27000000 INFO @ Thu, 16 Apr 2020 02:44:12: 22000000 INFO @ Thu, 16 Apr 2020 02:44:13: 28000000 INFO @ Thu, 16 Apr 2020 02:44:17: 23000000 INFO @ Thu, 16 Apr 2020 02:44:17: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:44:17: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:44:17: #1 total tags in treatment: 28867722 INFO @ Thu, 16 Apr 2020 02:44:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:44:17: #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 02:44:18: #1 tags after filtering in treatment: 28867722 INFO @ Thu, 16 Apr 2020 02:44:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:44:18: #1 finished! INFO @ Thu, 16 Apr 2020 02:44:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:44:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:44:20: #2 number of paired peaks: 465 WARNING @ Thu, 16 Apr 2020 02:44:20: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Thu, 16 Apr 2020 02:44:20: start model_add_line... INFO @ Thu, 16 Apr 2020 02:44:20: start X-correlation... INFO @ Thu, 16 Apr 2020 02:44:20: end of X-cor INFO @ Thu, 16 Apr 2020 02:44:20: #2 finished! INFO @ Thu, 16 Apr 2020 02:44:20: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:44:20: #2 alternative fragment length(s) may be 1,16,29 bps INFO @ Thu, 16 Apr 2020 02:44:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.10_model.r WARNING @ Thu, 16 Apr 2020 02:44:20: #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 02:44:20: #2 You may need to consider one of the other alternative d(s): 1,16,29 WARNING @ Thu, 16 Apr 2020 02:44:20: #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 02:44:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:44:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:44:22: 24000000 INFO @ Thu, 16 Apr 2020 02:44:27: 25000000 INFO @ Thu, 16 Apr 2020 02:44:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:44:32: 26000000 INFO @ Thu, 16 Apr 2020 02:44:37: 27000000 INFO @ Thu, 16 Apr 2020 02:44:41: 28000000 INFO @ Thu, 16 Apr 2020 02:44:46: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:44:46: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:44:46: #1 total tags in treatment: 28867722 INFO @ Thu, 16 Apr 2020 02:44:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:44:46: #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 02:44:46: #1 tags after filtering in treatment: 28867722 INFO @ Thu, 16 Apr 2020 02:44:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:44:46: #1 finished! INFO @ Thu, 16 Apr 2020 02:44:46: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:44:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:44:48: #2 number of paired peaks: 465 WARNING @ Thu, 16 Apr 2020 02:44:48: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Thu, 16 Apr 2020 02:44:48: start model_add_line... INFO @ Thu, 16 Apr 2020 02:44:48: start X-correlation... INFO @ Thu, 16 Apr 2020 02:44:48: end of X-cor INFO @ Thu, 16 Apr 2020 02:44:48: #2 finished! INFO @ Thu, 16 Apr 2020 02:44:48: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:44:48: #2 alternative fragment length(s) may be 1,16,29 bps INFO @ Thu, 16 Apr 2020 02:44:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.20_model.r WARNING @ Thu, 16 Apr 2020 02:44:48: #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 02:44:48: #2 You may need to consider one of the other alternative d(s): 1,16,29 WARNING @ Thu, 16 Apr 2020 02:44:48: #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 02:44:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:44:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:44:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:44:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.05_summits.bed INFO @ Thu, 16 Apr 2020 02:44:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:45:06: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:45:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:45:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:45:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.10_summits.bed INFO @ Thu, 16 Apr 2020 02:45:27: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:45:32: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:45:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:45:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:45:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436038/SRX5436038.20_summits.bed INFO @ Thu, 16 Apr 2020 02:45:53: Done! pass1 - making usageList (0 chroms): 0 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。