Job ID = 5720875 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:47:16 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 ) 2020-04-15T17:50:23 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 : 45,774,333 reads read : 45,774,333 reads written : 45,774,333 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: 00:13:52 45774333 reads; of these: 45774333 (100.00%) were unpaired; of these: 1892491 (4.13%) aligned 0 times 30998784 (67.72%) aligned exactly 1 time 12883058 (28.14%) aligned >1 times 95.87% overall alignment rate Time searching: 00:13:52 Overall time: 00:13:52 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 20 files... [bam_rmdupse_core] 8204795 / 43881842 = 0.1870 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 03:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.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 03:23:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:23:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:23:54: 1000000 INFO @ Thu, 16 Apr 2020 03:23:59: 2000000 INFO @ Thu, 16 Apr 2020 03:24:04: 3000000 INFO @ Thu, 16 Apr 2020 03:24:09: 4000000 INFO @ Thu, 16 Apr 2020 03:24:15: 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 03:24:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.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 03:24:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:24:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:24:20: 6000000 INFO @ Thu, 16 Apr 2020 03:24:24: 1000000 INFO @ Thu, 16 Apr 2020 03:24:25: 7000000 INFO @ Thu, 16 Apr 2020 03:24:29: 2000000 INFO @ Thu, 16 Apr 2020 03:24:31: 8000000 INFO @ Thu, 16 Apr 2020 03:24:34: 3000000 INFO @ Thu, 16 Apr 2020 03:24:36: 9000000 INFO @ Thu, 16 Apr 2020 03:24:40: 4000000 INFO @ Thu, 16 Apr 2020 03:24:42: 10000000 INFO @ Thu, 16 Apr 2020 03:24:45: 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 03:24:47: 11000000 INFO @ Thu, 16 Apr 2020 03:24:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.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 03:24:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:24:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:24:50: 6000000 INFO @ Thu, 16 Apr 2020 03:24:53: 12000000 INFO @ Thu, 16 Apr 2020 03:24:54: 1000000 INFO @ Thu, 16 Apr 2020 03:24:56: 7000000 INFO @ Thu, 16 Apr 2020 03:24:58: 13000000 INFO @ Thu, 16 Apr 2020 03:24:59: 2000000 INFO @ Thu, 16 Apr 2020 03:25:01: 8000000 INFO @ Thu, 16 Apr 2020 03:25:03: 14000000 INFO @ Thu, 16 Apr 2020 03:25:04: 3000000 INFO @ Thu, 16 Apr 2020 03:25:06: 9000000 INFO @ Thu, 16 Apr 2020 03:25:09: 15000000 INFO @ Thu, 16 Apr 2020 03:25:09: 4000000 INFO @ Thu, 16 Apr 2020 03:25:11: 10000000 INFO @ Thu, 16 Apr 2020 03:25:14: 16000000 INFO @ Thu, 16 Apr 2020 03:25:15: 5000000 INFO @ Thu, 16 Apr 2020 03:25:17: 11000000 INFO @ Thu, 16 Apr 2020 03:25:20: 17000000 INFO @ Thu, 16 Apr 2020 03:25:20: 6000000 INFO @ Thu, 16 Apr 2020 03:25:22: 12000000 INFO @ Thu, 16 Apr 2020 03:25:25: 7000000 INFO @ Thu, 16 Apr 2020 03:25:25: 18000000 INFO @ Thu, 16 Apr 2020 03:25:27: 13000000 INFO @ Thu, 16 Apr 2020 03:25:30: 8000000 INFO @ Thu, 16 Apr 2020 03:25:31: 19000000 INFO @ Thu, 16 Apr 2020 03:25:32: 14000000 INFO @ Thu, 16 Apr 2020 03:25:36: 9000000 INFO @ Thu, 16 Apr 2020 03:25:36: 20000000 INFO @ Thu, 16 Apr 2020 03:25:38: 15000000 INFO @ Thu, 16 Apr 2020 03:25:41: 10000000 INFO @ Thu, 16 Apr 2020 03:25:41: 21000000 INFO @ Thu, 16 Apr 2020 03:25:43: 16000000 INFO @ Thu, 16 Apr 2020 03:25:46: 11000000 INFO @ Thu, 16 Apr 2020 03:25:47: 22000000 INFO @ Thu, 16 Apr 2020 03:25:48: 17000000 INFO @ Thu, 16 Apr 2020 03:25:51: 12000000 INFO @ Thu, 16 Apr 2020 03:25:52: 23000000 INFO @ Thu, 16 Apr 2020 03:25:53: 18000000 INFO @ Thu, 16 Apr 2020 03:25:57: 13000000 INFO @ Thu, 16 Apr 2020 03:25:58: 24000000 INFO @ Thu, 16 Apr 2020 03:25:59: 19000000 INFO @ Thu, 16 Apr 2020 03:26:02: 14000000 INFO @ Thu, 16 Apr 2020 03:26:03: 25000000 INFO @ Thu, 16 Apr 2020 03:26:04: 20000000 INFO @ Thu, 16 Apr 2020 03:26:07: 15000000 INFO @ Thu, 16 Apr 2020 03:26:09: 26000000 INFO @ Thu, 16 Apr 2020 03:26:10: 21000000 INFO @ Thu, 16 Apr 2020 03:26:13: 16000000 INFO @ Thu, 16 Apr 2020 03:26:14: 27000000 INFO @ Thu, 16 Apr 2020 03:26:15: 22000000 INFO @ Thu, 16 Apr 2020 03:26:18: 17000000 INFO @ Thu, 16 Apr 2020 03:26:19: 28000000 INFO @ Thu, 16 Apr 2020 03:26:20: 23000000 INFO @ Thu, 16 Apr 2020 03:26:23: 18000000 INFO @ Thu, 16 Apr 2020 03:26:25: 29000000 INFO @ Thu, 16 Apr 2020 03:26:26: 24000000 INFO @ Thu, 16 Apr 2020 03:26:29: 19000000 INFO @ Thu, 16 Apr 2020 03:26:30: 30000000 INFO @ Thu, 16 Apr 2020 03:26:31: 25000000 INFO @ Thu, 16 Apr 2020 03:26:34: 20000000 INFO @ Thu, 16 Apr 2020 03:26:35: 31000000 INFO @ Thu, 16 Apr 2020 03:26:36: 26000000 INFO @ Thu, 16 Apr 2020 03:26:39: 21000000 INFO @ Thu, 16 Apr 2020 03:26:40: 32000000 INFO @ Thu, 16 Apr 2020 03:26:42: 27000000 INFO @ Thu, 16 Apr 2020 03:26:45: 22000000 INFO @ Thu, 16 Apr 2020 03:26:45: 33000000 INFO @ Thu, 16 Apr 2020 03:26:47: 28000000 INFO @ Thu, 16 Apr 2020 03:26:50: 23000000 INFO @ Thu, 16 Apr 2020 03:26:51: 34000000 INFO @ Thu, 16 Apr 2020 03:26:52: 29000000 INFO @ Thu, 16 Apr 2020 03:26:55: 24000000 INFO @ Thu, 16 Apr 2020 03:26:56: 35000000 INFO @ Thu, 16 Apr 2020 03:26:58: 30000000 INFO @ Thu, 16 Apr 2020 03:27:00: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:27:00: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:27:00: #1 total tags in treatment: 35677047 INFO @ Thu, 16 Apr 2020 03:27:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:27:00: #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 03:27:00: #1 tags after filtering in treatment: 35677047 INFO @ Thu, 16 Apr 2020 03:27:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:27:00: #1 finished! INFO @ Thu, 16 Apr 2020 03:27:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:27:01: 25000000 INFO @ Thu, 16 Apr 2020 03:27:02: #2 number of paired peaks: 223 WARNING @ Thu, 16 Apr 2020 03:27:02: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Thu, 16 Apr 2020 03:27:02: start model_add_line... INFO @ Thu, 16 Apr 2020 03:27:02: start X-correlation... INFO @ Thu, 16 Apr 2020 03:27:02: end of X-cor INFO @ Thu, 16 Apr 2020 03:27:02: #2 finished! INFO @ Thu, 16 Apr 2020 03:27:02: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 03:27:02: #2 alternative fragment length(s) may be 1,28 bps INFO @ Thu, 16 Apr 2020 03:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.05_model.r WARNING @ Thu, 16 Apr 2020 03:27:02: #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 03:27:02: #2 You may need to consider one of the other alternative d(s): 1,28 WARNING @ Thu, 16 Apr 2020 03:27:02: #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 03:27:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:27:03: 31000000 INFO @ Thu, 16 Apr 2020 03:27:06: 26000000 INFO @ Thu, 16 Apr 2020 03:27:08: 32000000 INFO @ Thu, 16 Apr 2020 03:27:11: 27000000 INFO @ Thu, 16 Apr 2020 03:27:13: 33000000 INFO @ Thu, 16 Apr 2020 03:27:17: 28000000 INFO @ Thu, 16 Apr 2020 03:27:18: 34000000 INFO @ Thu, 16 Apr 2020 03:27:22: 29000000 INFO @ Thu, 16 Apr 2020 03:27:23: 35000000 INFO @ Thu, 16 Apr 2020 03:27:27: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:27:27: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:27:27: #1 total tags in treatment: 35677047 INFO @ Thu, 16 Apr 2020 03:27:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:27:27: #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 03:27:27: 30000000 INFO @ Thu, 16 Apr 2020 03:27:27: #1 tags after filtering in treatment: 35677047 INFO @ Thu, 16 Apr 2020 03:27:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:27:27: #1 finished! INFO @ Thu, 16 Apr 2020 03:27:27: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:27:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:27:30: #2 number of paired peaks: 223 WARNING @ Thu, 16 Apr 2020 03:27:30: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Thu, 16 Apr 2020 03:27:30: start model_add_line... INFO @ Thu, 16 Apr 2020 03:27:30: start X-correlation... INFO @ Thu, 16 Apr 2020 03:27:30: end of X-cor INFO @ Thu, 16 Apr 2020 03:27:30: #2 finished! INFO @ Thu, 16 Apr 2020 03:27:30: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 03:27:30: #2 alternative fragment length(s) may be 1,28 bps INFO @ Thu, 16 Apr 2020 03:27:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.10_model.r WARNING @ Thu, 16 Apr 2020 03:27:30: #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 03:27:30: #2 You may need to consider one of the other alternative d(s): 1,28 WARNING @ Thu, 16 Apr 2020 03:27:30: #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 03:27:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:27:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:27:32: 31000000 INFO @ Thu, 16 Apr 2020 03:27:37: 32000000 INFO @ Thu, 16 Apr 2020 03:27:42: 33000000 INFO @ Thu, 16 Apr 2020 03:27:47: 34000000 INFO @ Thu, 16 Apr 2020 03:27:52: 35000000 INFO @ Thu, 16 Apr 2020 03:27:56: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:27:56: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:27:56: #1 total tags in treatment: 35677047 INFO @ Thu, 16 Apr 2020 03:27:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:27:56: #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 03:27:56: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:27:56: #1 tags after filtering in treatment: 35677047 INFO @ Thu, 16 Apr 2020 03:27:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:27:56: #1 finished! INFO @ Thu, 16 Apr 2020 03:27:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:27:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:27:59: #2 number of paired peaks: 223 WARNING @ Thu, 16 Apr 2020 03:27:59: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Thu, 16 Apr 2020 03:27:59: start model_add_line... INFO @ Thu, 16 Apr 2020 03:27:59: start X-correlation... INFO @ Thu, 16 Apr 2020 03:27:59: end of X-cor INFO @ Thu, 16 Apr 2020 03:27:59: #2 finished! INFO @ Thu, 16 Apr 2020 03:27:59: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 03:27:59: #2 alternative fragment length(s) may be 1,28 bps INFO @ Thu, 16 Apr 2020 03:27:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.20_model.r WARNING @ Thu, 16 Apr 2020 03:27:59: #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 03:27:59: #2 You may need to consider one of the other alternative d(s): 1,28 WARNING @ Thu, 16 Apr 2020 03:27:59: #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 03:27:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:27:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:28:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:28:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:28:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.05_summits.bed INFO @ Thu, 16 Apr 2020 03:28:19: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:28:22: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:28:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:28:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:28:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.10_summits.bed INFO @ Thu, 16 Apr 2020 03:28:46: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:28:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436061/SRX5436061.20_summits.bed INFO @ Thu, 16 Apr 2020 03:29:16: 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。