Job ID = 5720147 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T12:12:11 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 ) 2020-04-15T12:12:59 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 ) 2020-04-15T12:12:59 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 ) 2020-04-15T12:12:59 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 ) spots read : 25,796,593 reads read : 51,593,186 reads written : 25,796,593 reads 0-length : 25,796,593 spots read : 20,784,388 reads read : 41,568,776 reads written : 20,784,388 reads 0-length : 20,784,388 spots read : 49,989,487 reads read : 99,978,974 reads written : 49,989,487 reads 0-length : 49,989,487 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: 00:19:27 96570468 reads; of these: 96570468 (100.00%) were unpaired; of these: 30116082 (31.19%) aligned 0 times 52045180 (53.89%) aligned exactly 1 time 14409206 (14.92%) aligned >1 times 68.81% overall alignment rate Time searching: 00:19:27 Overall time: 00:19:28 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 28 files... [bam_rmdupse_core] 41237104 / 66454386 = 0.6205 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 22:27:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.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 22:27:04: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:27:04: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:27:09: 1000000 INFO @ Wed, 15 Apr 2020 22:27:15: 2000000 INFO @ Wed, 15 Apr 2020 22:27:20: 3000000 INFO @ Wed, 15 Apr 2020 22:27:25: 4000000 INFO @ Wed, 15 Apr 2020 22:27:30: 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 @ Wed, 15 Apr 2020 22:27:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.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 22:27:34: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:27:34: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:27:35: 6000000 INFO @ Wed, 15 Apr 2020 22:27:40: 1000000 INFO @ Wed, 15 Apr 2020 22:27:40: 7000000 INFO @ Wed, 15 Apr 2020 22:27:46: 8000000 INFO @ Wed, 15 Apr 2020 22:27:46: 2000000 INFO @ Wed, 15 Apr 2020 22:27:52: 9000000 INFO @ Wed, 15 Apr 2020 22:27:53: 3000000 INFO @ Wed, 15 Apr 2020 22:27:57: 10000000 INFO @ Wed, 15 Apr 2020 22:27:59: 4000000 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 22:28:03: 11000000 INFO @ Wed, 15 Apr 2020 22:28:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.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 22:28:04: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:28:04: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:28:05: 5000000 INFO @ Wed, 15 Apr 2020 22:28:08: 12000000 INFO @ Wed, 15 Apr 2020 22:28:09: 1000000 INFO @ Wed, 15 Apr 2020 22:28:12: 6000000 INFO @ Wed, 15 Apr 2020 22:28:14: 13000000 INFO @ Wed, 15 Apr 2020 22:28:15: 2000000 INFO @ Wed, 15 Apr 2020 22:28:18: 7000000 INFO @ Wed, 15 Apr 2020 22:28:19: 14000000 INFO @ Wed, 15 Apr 2020 22:28:20: 3000000 INFO @ Wed, 15 Apr 2020 22:28:24: 8000000 INFO @ Wed, 15 Apr 2020 22:28:25: 15000000 INFO @ Wed, 15 Apr 2020 22:28:26: 4000000 INFO @ Wed, 15 Apr 2020 22:28:30: 16000000 INFO @ Wed, 15 Apr 2020 22:28:30: 9000000 INFO @ Wed, 15 Apr 2020 22:28:31: 5000000 INFO @ Wed, 15 Apr 2020 22:28:36: 17000000 INFO @ Wed, 15 Apr 2020 22:28:37: 10000000 INFO @ Wed, 15 Apr 2020 22:28:37: 6000000 INFO @ Wed, 15 Apr 2020 22:28:41: 18000000 INFO @ Wed, 15 Apr 2020 22:28:42: 7000000 INFO @ Wed, 15 Apr 2020 22:28:43: 11000000 INFO @ Wed, 15 Apr 2020 22:28:47: 19000000 INFO @ Wed, 15 Apr 2020 22:28:48: 8000000 INFO @ Wed, 15 Apr 2020 22:28:49: 12000000 INFO @ Wed, 15 Apr 2020 22:28:52: 20000000 INFO @ Wed, 15 Apr 2020 22:28:53: 9000000 INFO @ Wed, 15 Apr 2020 22:28:55: 13000000 INFO @ Wed, 15 Apr 2020 22:28:58: 21000000 INFO @ Wed, 15 Apr 2020 22:28:59: 10000000 INFO @ Wed, 15 Apr 2020 22:29:02: 14000000 INFO @ Wed, 15 Apr 2020 22:29:03: 22000000 INFO @ Wed, 15 Apr 2020 22:29:04: 11000000 INFO @ Wed, 15 Apr 2020 22:29:08: 15000000 INFO @ Wed, 15 Apr 2020 22:29:09: 23000000 INFO @ Wed, 15 Apr 2020 22:29:10: 12000000 INFO @ Wed, 15 Apr 2020 22:29:14: 24000000 INFO @ Wed, 15 Apr 2020 22:29:14: 16000000 INFO @ Wed, 15 Apr 2020 22:29:15: 13000000 INFO @ Wed, 15 Apr 2020 22:29:20: 25000000 INFO @ Wed, 15 Apr 2020 22:29:21: 17000000 INFO @ Wed, 15 Apr 2020 22:29:21: 14000000 INFO @ Wed, 15 Apr 2020 22:29:21: #1 tag size is determined as 58 bps INFO @ Wed, 15 Apr 2020 22:29:21: #1 tag size = 58 INFO @ Wed, 15 Apr 2020 22:29:21: #1 total tags in treatment: 25217282 INFO @ Wed, 15 Apr 2020 22:29:21: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:29:21: #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 22:29:21: #1 tags after filtering in treatment: 25217282 INFO @ Wed, 15 Apr 2020 22:29:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:29:21: #1 finished! INFO @ Wed, 15 Apr 2020 22:29:21: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:29:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:29:23: #2 number of paired peaks: 180 WARNING @ Wed, 15 Apr 2020 22:29:23: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Wed, 15 Apr 2020 22:29:23: start model_add_line... INFO @ Wed, 15 Apr 2020 22:29:23: start X-correlation... INFO @ Wed, 15 Apr 2020 22:29:23: end of X-cor INFO @ Wed, 15 Apr 2020 22:29:23: #2 finished! INFO @ Wed, 15 Apr 2020 22:29:23: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:29:23: #2 alternative fragment length(s) may be 1,29,47,497,522,557 bps INFO @ Wed, 15 Apr 2020 22:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.05_model.r WARNING @ Wed, 15 Apr 2020 22:29:23: #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 22:29:23: #2 You may need to consider one of the other alternative d(s): 1,29,47,497,522,557 WARNING @ Wed, 15 Apr 2020 22:29:23: #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 22:29:23: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:29:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:29:26: 15000000 INFO @ Wed, 15 Apr 2020 22:29:27: 18000000 INFO @ Wed, 15 Apr 2020 22:29:32: 16000000 INFO @ Wed, 15 Apr 2020 22:29:33: 19000000 INFO @ Wed, 15 Apr 2020 22:29:37: 17000000 INFO @ Wed, 15 Apr 2020 22:29:39: 20000000 INFO @ Wed, 15 Apr 2020 22:29:43: 18000000 INFO @ Wed, 15 Apr 2020 22:29:45: 21000000 INFO @ Wed, 15 Apr 2020 22:29:48: 19000000 INFO @ Wed, 15 Apr 2020 22:29:52: 22000000 INFO @ Wed, 15 Apr 2020 22:29:54: 20000000 INFO @ Wed, 15 Apr 2020 22:29:58: 23000000 INFO @ Wed, 15 Apr 2020 22:29:59: 21000000 INFO @ Wed, 15 Apr 2020 22:30:00: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:30:04: 24000000 INFO @ Wed, 15 Apr 2020 22:30:05: 22000000 INFO @ Wed, 15 Apr 2020 22:30:10: 25000000 INFO @ Wed, 15 Apr 2020 22:30:10: 23000000 INFO @ Wed, 15 Apr 2020 22:30:12: #1 tag size is determined as 58 bps INFO @ Wed, 15 Apr 2020 22:30:12: #1 tag size = 58 INFO @ Wed, 15 Apr 2020 22:30:12: #1 total tags in treatment: 25217282 INFO @ Wed, 15 Apr 2020 22:30:12: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:30:12: #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 22:30:12: #1 tags after filtering in treatment: 25217282 INFO @ Wed, 15 Apr 2020 22:30:12: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:30:12: #1 finished! INFO @ Wed, 15 Apr 2020 22:30:12: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:30:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:30:14: #2 number of paired peaks: 180 WARNING @ Wed, 15 Apr 2020 22:30:14: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Wed, 15 Apr 2020 22:30:14: start model_add_line... INFO @ Wed, 15 Apr 2020 22:30:14: start X-correlation... INFO @ Wed, 15 Apr 2020 22:30:14: end of X-cor INFO @ Wed, 15 Apr 2020 22:30:14: #2 finished! INFO @ Wed, 15 Apr 2020 22:30:14: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:30:14: #2 alternative fragment length(s) may be 1,29,47,497,522,557 bps INFO @ Wed, 15 Apr 2020 22:30:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.10_model.r WARNING @ Wed, 15 Apr 2020 22:30:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:30:14: #2 You may need to consider one of the other alternative d(s): 1,29,47,497,522,557 WARNING @ Wed, 15 Apr 2020 22:30:14: #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 22:30:14: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:30:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:30:16: 24000000 INFO @ Wed, 15 Apr 2020 22:30:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:30:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:30:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.05_summits.bed INFO @ Wed, 15 Apr 2020 22:30:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:30:21: 25000000 INFO @ Wed, 15 Apr 2020 22:30:23: #1 tag size is determined as 58 bps INFO @ Wed, 15 Apr 2020 22:30:23: #1 tag size = 58 INFO @ Wed, 15 Apr 2020 22:30:23: #1 total tags in treatment: 25217282 INFO @ Wed, 15 Apr 2020 22:30:23: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:30:23: #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 22:30:23: #1 tags after filtering in treatment: 25217282 INFO @ Wed, 15 Apr 2020 22:30:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:30:23: #1 finished! INFO @ Wed, 15 Apr 2020 22:30:23: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:30:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:30:25: #2 number of paired peaks: 180 WARNING @ Wed, 15 Apr 2020 22:30:25: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Wed, 15 Apr 2020 22:30:25: start model_add_line... INFO @ Wed, 15 Apr 2020 22:30:25: start X-correlation... INFO @ Wed, 15 Apr 2020 22:30:25: end of X-cor INFO @ Wed, 15 Apr 2020 22:30:25: #2 finished! INFO @ Wed, 15 Apr 2020 22:30:25: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:30:25: #2 alternative fragment length(s) may be 1,29,47,497,522,557 bps INFO @ Wed, 15 Apr 2020 22:30:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.20_model.r WARNING @ Wed, 15 Apr 2020 22:30:25: #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 22:30:25: #2 You may need to consider one of the other alternative d(s): 1,29,47,497,522,557 WARNING @ Wed, 15 Apr 2020 22:30:25: #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 22:30:25: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:30:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:30:51: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:31:01: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.10_summits.bed INFO @ Wed, 15 Apr 2020 22:31:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:31:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:31:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:31:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702590/SRX5702590.20_summits.bed INFO @ Wed, 15 Apr 2020 22:31:18: 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。