Job ID = 5720338 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T14:45:01 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 ) 2020-04-15T14:45:01 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 ) 2020-04-15T14:45:01 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 : 32,221,758 reads read : 32,221,758 reads written : 32,221,758 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 32221758 reads; of these: 32221758 (100.00%) were unpaired; of these: 1325684 (4.11%) aligned 0 times 23555190 (73.10%) aligned exactly 1 time 7340884 (22.78%) aligned >1 times 95.89% 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: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 6948191 / 30896074 = 0.2249 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 00:17:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.bam'] # control file = None # effective genome size = 9.00e+07 # 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 00:17:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:17:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:17:28: 1000000 INFO @ Thu, 16 Apr 2020 00:17:35: 2000000 INFO @ Thu, 16 Apr 2020 00:17:42: 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 00:17:49: 4000000 INFO @ Thu, 16 Apr 2020 00:17:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.bam'] # control file = None # effective genome size = 9.00e+07 # 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 00:17:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:17:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:17:56: 5000000 INFO @ Thu, 16 Apr 2020 00:17:58: 1000000 INFO @ Thu, 16 Apr 2020 00:18:04: 6000000 INFO @ Thu, 16 Apr 2020 00:18:06: 2000000 INFO @ Thu, 16 Apr 2020 00:18:11: 7000000 INFO @ Thu, 16 Apr 2020 00:18:14: 3000000 INFO @ Thu, 16 Apr 2020 00:18:19: 8000000 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 00:18:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.bam'] # control file = None # effective genome size = 9.00e+07 # 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 00:18:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:18:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:18:21: 4000000 INFO @ Thu, 16 Apr 2020 00:18:26: 9000000 INFO @ Thu, 16 Apr 2020 00:18:28: 1000000 INFO @ Thu, 16 Apr 2020 00:18:29: 5000000 INFO @ Thu, 16 Apr 2020 00:18:34: 10000000 INFO @ Thu, 16 Apr 2020 00:18:35: 2000000 INFO @ Thu, 16 Apr 2020 00:18:37: 6000000 INFO @ Thu, 16 Apr 2020 00:18:41: 11000000 INFO @ Thu, 16 Apr 2020 00:18:42: 3000000 INFO @ Thu, 16 Apr 2020 00:18:44: 7000000 INFO @ Thu, 16 Apr 2020 00:18:48: 12000000 INFO @ Thu, 16 Apr 2020 00:18:49: 4000000 INFO @ Thu, 16 Apr 2020 00:18:52: 8000000 INFO @ Thu, 16 Apr 2020 00:18:55: 13000000 INFO @ Thu, 16 Apr 2020 00:18:56: 5000000 INFO @ Thu, 16 Apr 2020 00:19:00: 9000000 INFO @ Thu, 16 Apr 2020 00:19:02: 14000000 INFO @ Thu, 16 Apr 2020 00:19:03: 6000000 INFO @ Thu, 16 Apr 2020 00:19:07: 10000000 INFO @ Thu, 16 Apr 2020 00:19:09: 15000000 INFO @ Thu, 16 Apr 2020 00:19:10: 7000000 INFO @ Thu, 16 Apr 2020 00:19:15: 11000000 INFO @ Thu, 16 Apr 2020 00:19:16: 16000000 INFO @ Thu, 16 Apr 2020 00:19:16: 8000000 INFO @ Thu, 16 Apr 2020 00:19:23: 12000000 INFO @ Thu, 16 Apr 2020 00:19:23: 17000000 INFO @ Thu, 16 Apr 2020 00:19:23: 9000000 INFO @ Thu, 16 Apr 2020 00:19:30: 18000000 INFO @ Thu, 16 Apr 2020 00:19:30: 13000000 INFO @ Thu, 16 Apr 2020 00:19:30: 10000000 INFO @ Thu, 16 Apr 2020 00:19:37: 19000000 INFO @ Thu, 16 Apr 2020 00:19:37: 11000000 INFO @ Thu, 16 Apr 2020 00:19:38: 14000000 INFO @ Thu, 16 Apr 2020 00:19:44: 20000000 INFO @ Thu, 16 Apr 2020 00:19:44: 12000000 INFO @ Thu, 16 Apr 2020 00:19:45: 15000000 INFO @ Thu, 16 Apr 2020 00:19:51: 21000000 INFO @ Thu, 16 Apr 2020 00:19:51: 13000000 INFO @ Thu, 16 Apr 2020 00:19:53: 16000000 INFO @ Thu, 16 Apr 2020 00:19:58: 22000000 INFO @ Thu, 16 Apr 2020 00:19:58: 14000000 INFO @ Thu, 16 Apr 2020 00:20:00: 17000000 INFO @ Thu, 16 Apr 2020 00:20:05: 23000000 INFO @ Thu, 16 Apr 2020 00:20:05: 15000000 INFO @ Thu, 16 Apr 2020 00:20:08: 18000000 INFO @ Thu, 16 Apr 2020 00:20:12: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:20:12: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:20:12: #1 total tags in treatment: 23947883 INFO @ Thu, 16 Apr 2020 00:20:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:20:12: #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 00:20:12: #1 tags after filtering in treatment: 23947883 INFO @ Thu, 16 Apr 2020 00:20:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:20:12: #1 finished! INFO @ Thu, 16 Apr 2020 00:20:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:20:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:20:13: 16000000 INFO @ Thu, 16 Apr 2020 00:20:14: #2 number of paired peaks: 239 WARNING @ Thu, 16 Apr 2020 00:20:14: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Thu, 16 Apr 2020 00:20:14: start model_add_line... INFO @ Thu, 16 Apr 2020 00:20:14: start X-correlation... INFO @ Thu, 16 Apr 2020 00:20:14: end of X-cor INFO @ Thu, 16 Apr 2020 00:20:14: #2 finished! INFO @ Thu, 16 Apr 2020 00:20:14: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 00:20:14: #2 alternative fragment length(s) may be 1,20,67,588 bps INFO @ Thu, 16 Apr 2020 00:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.05_model.r WARNING @ Thu, 16 Apr 2020 00:20:14: #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 00:20:14: #2 You may need to consider one of the other alternative d(s): 1,20,67,588 WARNING @ Thu, 16 Apr 2020 00:20:14: #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 00:20:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:20:16: 19000000 INFO @ Thu, 16 Apr 2020 00:20:20: 17000000 INFO @ Thu, 16 Apr 2020 00:20:23: 20000000 INFO @ Thu, 16 Apr 2020 00:20:27: 18000000 INFO @ Thu, 16 Apr 2020 00:20:30: 21000000 INFO @ Thu, 16 Apr 2020 00:20:34: 19000000 INFO @ Thu, 16 Apr 2020 00:20:38: 22000000 INFO @ Thu, 16 Apr 2020 00:20:41: 20000000 INFO @ Thu, 16 Apr 2020 00:20:45: 23000000 INFO @ Thu, 16 Apr 2020 00:20:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:20:48: 21000000 INFO @ Thu, 16 Apr 2020 00:20:52: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:20:52: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:20:52: #1 total tags in treatment: 23947883 INFO @ Thu, 16 Apr 2020 00:20:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:20:52: #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 00:20:53: #1 tags after filtering in treatment: 23947883 INFO @ Thu, 16 Apr 2020 00:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:20:53: #1 finished! INFO @ Thu, 16 Apr 2020 00:20:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:20:54: #2 number of paired peaks: 239 WARNING @ Thu, 16 Apr 2020 00:20:54: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Thu, 16 Apr 2020 00:20:54: start model_add_line... INFO @ Thu, 16 Apr 2020 00:20:54: start X-correlation... INFO @ Thu, 16 Apr 2020 00:20:54: end of X-cor INFO @ Thu, 16 Apr 2020 00:20:54: #2 finished! INFO @ Thu, 16 Apr 2020 00:20:54: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 00:20:54: #2 alternative fragment length(s) may be 1,20,67,588 bps INFO @ Thu, 16 Apr 2020 00:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.10_model.r WARNING @ Thu, 16 Apr 2020 00:20:54: #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 00:20:54: #2 You may need to consider one of the other alternative d(s): 1,20,67,588 WARNING @ Thu, 16 Apr 2020 00:20:54: #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 00:20:54: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:20:55: 22000000 INFO @ Thu, 16 Apr 2020 00:21:01: 23000000 INFO @ Thu, 16 Apr 2020 00:21:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:21:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:21:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.05_summits.bed INFO @ Thu, 16 Apr 2020 00:21:01: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:21:07: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:21:07: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:21:07: #1 total tags in treatment: 23947883 INFO @ Thu, 16 Apr 2020 00:21:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:21:07: #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 00:21:07: #1 tags after filtering in treatment: 23947883 INFO @ Thu, 16 Apr 2020 00:21:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:21:07: #1 finished! INFO @ Thu, 16 Apr 2020 00:21:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:21:09: #2 number of paired peaks: 239 WARNING @ Thu, 16 Apr 2020 00:21:09: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Thu, 16 Apr 2020 00:21:09: start model_add_line... INFO @ Thu, 16 Apr 2020 00:21:09: start X-correlation... INFO @ Thu, 16 Apr 2020 00:21:09: end of X-cor INFO @ Thu, 16 Apr 2020 00:21:09: #2 finished! INFO @ Thu, 16 Apr 2020 00:21:09: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 00:21:09: #2 alternative fragment length(s) may be 1,20,67,588 bps INFO @ Thu, 16 Apr 2020 00:21:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.20_model.r WARNING @ Thu, 16 Apr 2020 00:21:09: #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 00:21:09: #2 You may need to consider one of the other alternative d(s): 1,20,67,588 WARNING @ Thu, 16 Apr 2020 00:21:09: #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 00:21:09: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:21:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:21:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:21:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:21:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:21:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:21:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.10_summits.bed INFO @ Thu, 16 Apr 2020 00:21:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:21:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:21:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:21:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971802/SRX7971802.20_summits.bed INFO @ Thu, 16 Apr 2020 00:21:56: 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。