Job ID = 5720229 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T13:04:12 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 ) 2020-04-15T13:16:03 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 ) 2020-04-15T13:16:03 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 ) 2020-04-15T13:16:03 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 ) 2020-04-15T13:16:05 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 : 15,914,497 reads read : 31,828,994 reads written : 31,828,994 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: 00:31:29 15914497 reads; of these: 15914497 (100.00%) were paired; of these: 6889165 (43.29%) aligned concordantly 0 times 7545450 (47.41%) aligned concordantly exactly 1 time 1479882 (9.30%) aligned concordantly >1 times ---- 6889165 pairs aligned concordantly 0 times; of these: 3846246 (55.83%) aligned discordantly 1 time ---- 3042919 pairs aligned 0 times concordantly or discordantly; of these: 6085838 mates make up the pairs; of these: 4809389 (79.03%) aligned 0 times 514206 (8.45%) aligned exactly 1 time 762243 (12.52%) aligned >1 times 84.89% overall alignment rate Time searching: 00:31:29 Overall time: 00:31:29 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 20 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 811300 / 12640779 = 0.0642 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 23:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.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 23:17:36: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:17:36: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:17:42: 1000000 INFO @ Wed, 15 Apr 2020 23:17:48: 2000000 INFO @ Wed, 15 Apr 2020 23:17:54: 3000000 INFO @ Wed, 15 Apr 2020 23:18:00: 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 23:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.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 23:18:05: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:18:05: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:18:06: 5000000 INFO @ Wed, 15 Apr 2020 23:18:12: 1000000 INFO @ Wed, 15 Apr 2020 23:18:12: 6000000 INFO @ Wed, 15 Apr 2020 23:18:18: 2000000 INFO @ Wed, 15 Apr 2020 23:18:18: 7000000 INFO @ Wed, 15 Apr 2020 23:18:24: 3000000 INFO @ Wed, 15 Apr 2020 23:18:24: 8000000 INFO @ Wed, 15 Apr 2020 23:18:30: 4000000 INFO @ Wed, 15 Apr 2020 23:18:30: 9000000 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 23:18:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.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 23:18:35: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:18:35: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:18:36: 5000000 INFO @ Wed, 15 Apr 2020 23:18:36: 10000000 INFO @ Wed, 15 Apr 2020 23:18:41: 1000000 INFO @ Wed, 15 Apr 2020 23:18:42: 6000000 INFO @ Wed, 15 Apr 2020 23:18:43: 11000000 INFO @ Wed, 15 Apr 2020 23:18:47: 2000000 INFO @ Wed, 15 Apr 2020 23:18:48: 7000000 INFO @ Wed, 15 Apr 2020 23:18:49: 12000000 INFO @ Wed, 15 Apr 2020 23:18:54: 3000000 INFO @ Wed, 15 Apr 2020 23:18:55: 8000000 INFO @ Wed, 15 Apr 2020 23:18:55: 13000000 INFO @ Wed, 15 Apr 2020 23:19:00: 4000000 INFO @ Wed, 15 Apr 2020 23:19:01: 9000000 INFO @ Wed, 15 Apr 2020 23:19:01: 14000000 INFO @ Wed, 15 Apr 2020 23:19:06: 5000000 INFO @ Wed, 15 Apr 2020 23:19:07: 15000000 INFO @ Wed, 15 Apr 2020 23:19:07: 10000000 INFO @ Wed, 15 Apr 2020 23:19:12: 6000000 INFO @ Wed, 15 Apr 2020 23:19:13: 16000000 INFO @ Wed, 15 Apr 2020 23:19:13: 11000000 INFO @ Wed, 15 Apr 2020 23:19:18: 7000000 INFO @ Wed, 15 Apr 2020 23:19:19: 17000000 INFO @ Wed, 15 Apr 2020 23:19:19: 12000000 INFO @ Wed, 15 Apr 2020 23:19:24: 8000000 INFO @ Wed, 15 Apr 2020 23:19:25: 18000000 INFO @ Wed, 15 Apr 2020 23:19:25: 13000000 INFO @ Wed, 15 Apr 2020 23:19:30: 9000000 INFO @ Wed, 15 Apr 2020 23:19:31: 19000000 INFO @ Wed, 15 Apr 2020 23:19:31: 14000000 INFO @ Wed, 15 Apr 2020 23:19:36: 10000000 INFO @ Wed, 15 Apr 2020 23:19:37: 20000000 INFO @ Wed, 15 Apr 2020 23:19:37: 15000000 INFO @ Wed, 15 Apr 2020 23:19:42: 11000000 INFO @ Wed, 15 Apr 2020 23:19:43: 21000000 INFO @ Wed, 15 Apr 2020 23:19:43: 16000000 INFO @ Wed, 15 Apr 2020 23:19:48: 12000000 INFO @ Wed, 15 Apr 2020 23:19:49: 22000000 INFO @ Wed, 15 Apr 2020 23:19:50: 17000000 INFO @ Wed, 15 Apr 2020 23:19:54: 13000000 INFO @ Wed, 15 Apr 2020 23:19:55: 23000000 INFO @ Wed, 15 Apr 2020 23:19:56: 18000000 INFO @ Wed, 15 Apr 2020 23:20:00: 14000000 INFO @ Wed, 15 Apr 2020 23:20:01: 24000000 INFO @ Wed, 15 Apr 2020 23:20:02: 19000000 INFO @ Wed, 15 Apr 2020 23:20:06: 15000000 INFO @ Wed, 15 Apr 2020 23:20:07: 25000000 INFO @ Wed, 15 Apr 2020 23:20:08: 20000000 INFO @ Wed, 15 Apr 2020 23:20:09: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 23:20:09: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 23:20:09: #1 total tags in treatment: 8419053 INFO @ Wed, 15 Apr 2020 23:20:09: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:20:09: #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 23:20:09: #1 tags after filtering in treatment: 7503183 INFO @ Wed, 15 Apr 2020 23:20:09: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 15 Apr 2020 23:20:09: #1 finished! INFO @ Wed, 15 Apr 2020 23:20:09: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:20:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:20:10: #2 number of paired peaks: 311 WARNING @ Wed, 15 Apr 2020 23:20:10: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Wed, 15 Apr 2020 23:20:10: start model_add_line... INFO @ Wed, 15 Apr 2020 23:20:10: start X-correlation... INFO @ Wed, 15 Apr 2020 23:20:10: end of X-cor INFO @ Wed, 15 Apr 2020 23:20:10: #2 finished! INFO @ Wed, 15 Apr 2020 23:20:10: #2 predicted fragment length is 200 bps INFO @ Wed, 15 Apr 2020 23:20:10: #2 alternative fragment length(s) may be 200 bps INFO @ Wed, 15 Apr 2020 23:20:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.05_model.r WARNING @ Wed, 15 Apr 2020 23:20:10: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:20:10: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Wed, 15 Apr 2020 23:20:10: #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 23:20:10: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:20:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:20:12: 16000000 INFO @ Wed, 15 Apr 2020 23:20:14: 21000000 INFO @ Wed, 15 Apr 2020 23:20:18: 17000000 INFO @ Wed, 15 Apr 2020 23:20:20: 22000000 INFO @ Wed, 15 Apr 2020 23:20:24: 18000000 INFO @ Wed, 15 Apr 2020 23:20:26: 23000000 INFO @ Wed, 15 Apr 2020 23:20:26: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:20:30: 19000000 INFO @ Wed, 15 Apr 2020 23:20:32: 24000000 INFO @ Wed, 15 Apr 2020 23:20:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:20:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:20:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.05_summits.bed INFO @ Wed, 15 Apr 2020 23:20:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (394 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:20:36: 20000000 INFO @ Wed, 15 Apr 2020 23:20:38: 25000000 INFO @ Wed, 15 Apr 2020 23:20:40: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 23:20:40: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 23:20:40: #1 total tags in treatment: 8419053 INFO @ Wed, 15 Apr 2020 23:20:40: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:20:40: #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 23:20:40: #1 tags after filtering in treatment: 7503183 INFO @ Wed, 15 Apr 2020 23:20:40: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 15 Apr 2020 23:20:40: #1 finished! INFO @ Wed, 15 Apr 2020 23:20:40: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:20:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:20:41: #2 number of paired peaks: 311 WARNING @ Wed, 15 Apr 2020 23:20:41: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Wed, 15 Apr 2020 23:20:41: start model_add_line... INFO @ Wed, 15 Apr 2020 23:20:41: start X-correlation... INFO @ Wed, 15 Apr 2020 23:20:41: end of X-cor INFO @ Wed, 15 Apr 2020 23:20:41: #2 finished! INFO @ Wed, 15 Apr 2020 23:20:41: #2 predicted fragment length is 200 bps INFO @ Wed, 15 Apr 2020 23:20:41: #2 alternative fragment length(s) may be 200 bps INFO @ Wed, 15 Apr 2020 23:20:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.10_model.r WARNING @ Wed, 15 Apr 2020 23:20:41: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:20:41: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Wed, 15 Apr 2020 23:20:41: #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 23:20:41: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:20:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:20:42: 21000000 INFO @ Wed, 15 Apr 2020 23:20:48: 22000000 INFO @ Wed, 15 Apr 2020 23:20:54: 23000000 INFO @ Wed, 15 Apr 2020 23:20:57: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:21:00: 24000000 INFO @ Wed, 15 Apr 2020 23:21:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:21:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:21:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.10_summits.bed INFO @ Wed, 15 Apr 2020 23:21:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (272 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:21:06: 25000000 INFO @ Wed, 15 Apr 2020 23:21:08: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 23:21:08: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 23:21:08: #1 total tags in treatment: 8419053 INFO @ Wed, 15 Apr 2020 23:21:08: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:21:08: #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 23:21:08: #1 tags after filtering in treatment: 7503183 INFO @ Wed, 15 Apr 2020 23:21:08: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 15 Apr 2020 23:21:08: #1 finished! INFO @ Wed, 15 Apr 2020 23:21:08: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:21:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:21:09: #2 number of paired peaks: 311 WARNING @ Wed, 15 Apr 2020 23:21:09: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Wed, 15 Apr 2020 23:21:09: start model_add_line... INFO @ Wed, 15 Apr 2020 23:21:09: start X-correlation... INFO @ Wed, 15 Apr 2020 23:21:09: end of X-cor INFO @ Wed, 15 Apr 2020 23:21:09: #2 finished! INFO @ Wed, 15 Apr 2020 23:21:09: #2 predicted fragment length is 200 bps INFO @ Wed, 15 Apr 2020 23:21:09: #2 alternative fragment length(s) may be 200 bps INFO @ Wed, 15 Apr 2020 23:21:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.20_model.r WARNING @ Wed, 15 Apr 2020 23:21:09: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:21:09: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Wed, 15 Apr 2020 23:21:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:21:09: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:21:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:21:25: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:21:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:21:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:21:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619601/SRX6619601.20_summits.bed INFO @ Wed, 15 Apr 2020 23:21:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (179 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。