Job ID = 5720313 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T14:04:26 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 ) 2020-04-15T14:05:19 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 ) 2020-04-15T14:05:49 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 ) 2020-04-15T14:07:02 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 ) 2020-04-15T14:07:02 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 ) 2020-04-15T14:08:32 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 ) 2020-04-15T14:12:07 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 : 25,839,740 reads read : 25,839,740 reads written : 25,839,740 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:48 25839740 reads; of these: 25839740 (100.00%) were unpaired; of these: 1338031 (5.18%) aligned 0 times 18060707 (69.90%) aligned exactly 1 time 6441002 (24.93%) aligned >1 times 94.82% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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 12 files... [bam_rmdupse_core] 4108577 / 24501709 = 0.1677 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 @ Wed, 15 Apr 2020 23:30:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.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 @ Wed, 15 Apr 2020 23:30:19: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:30:19: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:30:25: 1000000 INFO @ Wed, 15 Apr 2020 23:30:30: 2000000 INFO @ Wed, 15 Apr 2020 23:30:36: 3000000 INFO @ Wed, 15 Apr 2020 23:30:42: 4000000 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 @ Wed, 15 Apr 2020 23:30:47: 5000000 INFO @ Wed, 15 Apr 2020 23:30:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.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 @ Wed, 15 Apr 2020 23:30:48: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:30:48: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:30:53: 6000000 INFO @ Wed, 15 Apr 2020 23:30:54: 1000000 INFO @ Wed, 15 Apr 2020 23:30:58: 7000000 INFO @ Wed, 15 Apr 2020 23:30:59: 2000000 INFO @ Wed, 15 Apr 2020 23:31:04: 8000000 INFO @ Wed, 15 Apr 2020 23:31:04: 3000000 INFO @ Wed, 15 Apr 2020 23:31:09: 9000000 INFO @ Wed, 15 Apr 2020 23:31:10: 4000000 INFO @ Wed, 15 Apr 2020 23:31:15: 10000000 INFO @ Wed, 15 Apr 2020 23:31:15: 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 @ Wed, 15 Apr 2020 23:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.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 @ Wed, 15 Apr 2020 23:31:18: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:31:18: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:31:20: 11000000 INFO @ Wed, 15 Apr 2020 23:31:20: 6000000 INFO @ Wed, 15 Apr 2020 23:31:24: 1000000 INFO @ Wed, 15 Apr 2020 23:31:26: 12000000 INFO @ Wed, 15 Apr 2020 23:31:26: 7000000 INFO @ Wed, 15 Apr 2020 23:31:29: 2000000 INFO @ Wed, 15 Apr 2020 23:31:31: 13000000 INFO @ Wed, 15 Apr 2020 23:31:31: 8000000 INFO @ Wed, 15 Apr 2020 23:31:35: 3000000 INFO @ Wed, 15 Apr 2020 23:31:37: 14000000 INFO @ Wed, 15 Apr 2020 23:31:37: 9000000 INFO @ Wed, 15 Apr 2020 23:31:40: 4000000 INFO @ Wed, 15 Apr 2020 23:31:42: 10000000 INFO @ Wed, 15 Apr 2020 23:31:42: 15000000 INFO @ Wed, 15 Apr 2020 23:31:46: 5000000 INFO @ Wed, 15 Apr 2020 23:31:47: 11000000 INFO @ Wed, 15 Apr 2020 23:31:47: 16000000 INFO @ Wed, 15 Apr 2020 23:31:51: 6000000 INFO @ Wed, 15 Apr 2020 23:31:53: 12000000 INFO @ Wed, 15 Apr 2020 23:31:53: 17000000 INFO @ Wed, 15 Apr 2020 23:31:57: 7000000 INFO @ Wed, 15 Apr 2020 23:31:58: 13000000 INFO @ Wed, 15 Apr 2020 23:31:58: 18000000 INFO @ Wed, 15 Apr 2020 23:32:03: 8000000 INFO @ Wed, 15 Apr 2020 23:32:03: 14000000 INFO @ Wed, 15 Apr 2020 23:32:04: 19000000 INFO @ Wed, 15 Apr 2020 23:32:08: 9000000 INFO @ Wed, 15 Apr 2020 23:32:09: 15000000 INFO @ Wed, 15 Apr 2020 23:32:09: 20000000 INFO @ Wed, 15 Apr 2020 23:32:12: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:32:12: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:32:12: #1 total tags in treatment: 20393132 INFO @ Wed, 15 Apr 2020 23:32:12: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:32:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:32:12: #1 tags after filtering in treatment: 20393132 INFO @ Wed, 15 Apr 2020 23:32:12: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:32:12: #1 finished! INFO @ Wed, 15 Apr 2020 23:32:12: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:32:13: #2 number of paired peaks: 393 WARNING @ Wed, 15 Apr 2020 23:32:13: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Wed, 15 Apr 2020 23:32:13: start model_add_line... INFO @ Wed, 15 Apr 2020 23:32:13: start X-correlation... INFO @ Wed, 15 Apr 2020 23:32:13: end of X-cor INFO @ Wed, 15 Apr 2020 23:32:13: #2 finished! INFO @ Wed, 15 Apr 2020 23:32:13: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 23:32:13: #2 alternative fragment length(s) may be 1,34 bps INFO @ Wed, 15 Apr 2020 23:32:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.05_model.r WARNING @ Wed, 15 Apr 2020 23:32:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:32:13: #2 You may need to consider one of the other alternative d(s): 1,34 WARNING @ Wed, 15 Apr 2020 23:32:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:32:13: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:32:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:32:14: 10000000 INFO @ Wed, 15 Apr 2020 23:32:14: 16000000 INFO @ Wed, 15 Apr 2020 23:32:19: 11000000 INFO @ Wed, 15 Apr 2020 23:32:20: 17000000 INFO @ Wed, 15 Apr 2020 23:32:25: 12000000 INFO @ Wed, 15 Apr 2020 23:32:25: 18000000 INFO @ Wed, 15 Apr 2020 23:32:31: 13000000 INFO @ Wed, 15 Apr 2020 23:32:31: 19000000 INFO @ Wed, 15 Apr 2020 23:32:36: 14000000 INFO @ Wed, 15 Apr 2020 23:32:36: 20000000 INFO @ Wed, 15 Apr 2020 23:32:39: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:32:39: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:32:39: #1 total tags in treatment: 20393132 INFO @ Wed, 15 Apr 2020 23:32:39: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:32:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:32:39: #1 tags after filtering in treatment: 20393132 INFO @ Wed, 15 Apr 2020 23:32:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:32:39: #1 finished! INFO @ Wed, 15 Apr 2020 23:32:39: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:32:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:32:40: #2 number of paired peaks: 393 WARNING @ Wed, 15 Apr 2020 23:32:40: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Wed, 15 Apr 2020 23:32:40: start model_add_line... INFO @ Wed, 15 Apr 2020 23:32:40: start X-correlation... INFO @ Wed, 15 Apr 2020 23:32:40: end of X-cor INFO @ Wed, 15 Apr 2020 23:32:40: #2 finished! INFO @ Wed, 15 Apr 2020 23:32:41: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 23:32:41: #2 alternative fragment length(s) may be 1,34 bps INFO @ Wed, 15 Apr 2020 23:32:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.10_model.r WARNING @ Wed, 15 Apr 2020 23:32:41: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:32:41: #2 You may need to consider one of the other alternative d(s): 1,34 WARNING @ Wed, 15 Apr 2020 23:32:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:32:41: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:32:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:32:42: 15000000 INFO @ Wed, 15 Apr 2020 23:32:45: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:32:47: 16000000 INFO @ Wed, 15 Apr 2020 23:32:53: 17000000 INFO @ Wed, 15 Apr 2020 23:32:58: 18000000 INFO @ Wed, 15 Apr 2020 23:32:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:32:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:32:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.05_summits.bed INFO @ Wed, 15 Apr 2020 23:32:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:33:04: 19000000 INFO @ Wed, 15 Apr 2020 23:33:09: 20000000 INFO @ Wed, 15 Apr 2020 23:33:10: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:33:12: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:33:12: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:33:12: #1 total tags in treatment: 20393132 INFO @ Wed, 15 Apr 2020 23:33:12: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:33:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:33:12: #1 tags after filtering in treatment: 20393132 INFO @ Wed, 15 Apr 2020 23:33:12: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:33:12: #1 finished! INFO @ Wed, 15 Apr 2020 23:33:12: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:33:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:33:13: #2 number of paired peaks: 393 WARNING @ Wed, 15 Apr 2020 23:33:13: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Wed, 15 Apr 2020 23:33:13: start model_add_line... INFO @ Wed, 15 Apr 2020 23:33:13: start X-correlation... INFO @ Wed, 15 Apr 2020 23:33:13: end of X-cor INFO @ Wed, 15 Apr 2020 23:33:13: #2 finished! INFO @ Wed, 15 Apr 2020 23:33:13: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 23:33:13: #2 alternative fragment length(s) may be 1,34 bps INFO @ Wed, 15 Apr 2020 23:33:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.20_model.r WARNING @ Wed, 15 Apr 2020 23:33:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:33:13: #2 You may need to consider one of the other alternative d(s): 1,34 WARNING @ Wed, 15 Apr 2020 23:33:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:33:13: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:33:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:33:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:33:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:33:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.10_summits.bed INFO @ Wed, 15 Apr 2020 23:33:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:33:44: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:33:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:33:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:33:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627597/SRX7627597.20_summits.bed INFO @ Wed, 15 Apr 2020 23:33:59: 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。