Job ID = 10165635 SRX = SRX6799192 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34221432 spots for SRR10065399/SRR10065399.sra Written 34221432 spots for SRR10065399/SRR10065399.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165902 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:20 34221432 reads; of these: 34221432 (100.00%) were unpaired; of these: 1678525 (4.90%) aligned 0 times 22403048 (65.46%) aligned exactly 1 time 10139859 (29.63%) aligned >1 times 95.10% overall alignment rate Time searching: 00:08:20 Overall time: 00:08:20 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] 10713353 / 32542907 = 0.3292 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, 08 Oct 2020 19:47:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.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, 08 Oct 2020 19:47:22: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:22: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:29: 1000000 INFO @ Thu, 08 Oct 2020 19:47:35: 2000000 INFO @ Thu, 08 Oct 2020 19:47:42: 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, 08 Oct 2020 19:47:49: 4000000 INFO @ Thu, 08 Oct 2020 19:47:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.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, 08 Oct 2020 19:47:51: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:51: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:56: 5000000 INFO @ Thu, 08 Oct 2020 19:47:59: 1000000 INFO @ Thu, 08 Oct 2020 19:48:03: 6000000 INFO @ Thu, 08 Oct 2020 19:48:06: 2000000 INFO @ Thu, 08 Oct 2020 19:48:10: 7000000 INFO @ Thu, 08 Oct 2020 19:48:13: 3000000 INFO @ Thu, 08 Oct 2020 19:48:18: 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, 08 Oct 2020 19:48:21: 4000000 INFO @ Thu, 08 Oct 2020 19:48:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.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, 08 Oct 2020 19:48:22: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:48:22: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:48:25: 9000000 INFO @ Thu, 08 Oct 2020 19:48:28: 5000000 INFO @ Thu, 08 Oct 2020 19:48:29: 1000000 INFO @ Thu, 08 Oct 2020 19:48:32: 10000000 INFO @ Thu, 08 Oct 2020 19:48:36: 6000000 INFO @ Thu, 08 Oct 2020 19:48:37: 2000000 INFO @ Thu, 08 Oct 2020 19:48:40: 11000000 INFO @ Thu, 08 Oct 2020 19:48:43: 7000000 INFO @ Thu, 08 Oct 2020 19:48:45: 3000000 INFO @ Thu, 08 Oct 2020 19:48:47: 12000000 INFO @ Thu, 08 Oct 2020 19:48:51: 8000000 INFO @ Thu, 08 Oct 2020 19:48:52: 4000000 INFO @ Thu, 08 Oct 2020 19:48:55: 13000000 INFO @ Thu, 08 Oct 2020 19:48:59: 9000000 INFO @ Thu, 08 Oct 2020 19:49:00: 5000000 INFO @ Thu, 08 Oct 2020 19:49:02: 14000000 INFO @ Thu, 08 Oct 2020 19:49:07: 10000000 INFO @ Thu, 08 Oct 2020 19:49:08: 6000000 INFO @ Thu, 08 Oct 2020 19:49:09: 15000000 INFO @ Thu, 08 Oct 2020 19:49:15: 11000000 INFO @ Thu, 08 Oct 2020 19:49:15: 7000000 INFO @ Thu, 08 Oct 2020 19:49:17: 16000000 INFO @ Thu, 08 Oct 2020 19:49:23: 12000000 INFO @ Thu, 08 Oct 2020 19:49:23: 8000000 INFO @ Thu, 08 Oct 2020 19:49:24: 17000000 INFO @ Thu, 08 Oct 2020 19:49:31: 9000000 INFO @ Thu, 08 Oct 2020 19:49:31: 13000000 INFO @ Thu, 08 Oct 2020 19:49:32: 18000000 INFO @ Thu, 08 Oct 2020 19:49:38: 10000000 INFO @ Thu, 08 Oct 2020 19:49:39: 14000000 INFO @ Thu, 08 Oct 2020 19:49:39: 19000000 INFO @ Thu, 08 Oct 2020 19:49:46: 11000000 INFO @ Thu, 08 Oct 2020 19:49:47: 15000000 INFO @ Thu, 08 Oct 2020 19:49:47: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:49:54: 12000000 INFO @ Thu, 08 Oct 2020 19:49:54: 21000000 INFO @ Thu, 08 Oct 2020 19:49:55: 16000000 INFO @ Thu, 08 Oct 2020 19:50:01: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:50:01: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:50:01: #1 total tags in treatment: 21829554 INFO @ Thu, 08 Oct 2020 19:50:01: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:50:01: #1 tags after filtering in treatment: 21829554 INFO @ Thu, 08 Oct 2020 19:50:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:01: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:01: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:02: 13000000 INFO @ Thu, 08 Oct 2020 19:50:02: #2 number of paired peaks: 425 WARNING @ Thu, 08 Oct 2020 19:50:02: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:02: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:03: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:03: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:03: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:03: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:50:03: #2 alternative fragment length(s) may be 1,17,42 bps INFO @ Thu, 08 Oct 2020 19:50:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.05_model.r INFO @ Thu, 08 Oct 2020 19:50:03: 17000000 WARNING @ Thu, 08 Oct 2020 19:50:03: #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, 08 Oct 2020 19:50:03: #2 You may need to consider one of the other alternative d(s): 1,17,42 WARNING @ Thu, 08 Oct 2020 19:50:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:50:03: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:10: 14000000 INFO @ Thu, 08 Oct 2020 19:50:11: 18000000 INFO @ Thu, 08 Oct 2020 19:50:17: 15000000 INFO @ Thu, 08 Oct 2020 19:50:19: 19000000 INFO @ Thu, 08 Oct 2020 19:50:25: 16000000 INFO @ Thu, 08 Oct 2020 19:50:26: 20000000 INFO @ Thu, 08 Oct 2020 19:50:33: 17000000 INFO @ Thu, 08 Oct 2020 19:50:34: 21000000 INFO @ Thu, 08 Oct 2020 19:50:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:50:41: 18000000 INFO @ Thu, 08 Oct 2020 19:50:41: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:50:41: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:50:41: #1 total tags in treatment: 21829554 INFO @ Thu, 08 Oct 2020 19:50:41: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:50:41: #1 tags after filtering in treatment: 21829554 INFO @ Thu, 08 Oct 2020 19:50:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:41: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:41: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:42: #2 number of paired peaks: 425 WARNING @ Thu, 08 Oct 2020 19:50:42: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:42: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:43: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:43: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:43: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:43: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:50:43: #2 alternative fragment length(s) may be 1,17,42 bps INFO @ Thu, 08 Oct 2020 19:50:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.10_model.r WARNING @ Thu, 08 Oct 2020 19:50:43: #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, 08 Oct 2020 19:50:43: #2 You may need to consider one of the other alternative d(s): 1,17,42 WARNING @ Thu, 08 Oct 2020 19:50:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:50:43: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:48: 19000000 INFO @ Thu, 08 Oct 2020 19:50:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:50:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:50:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.05_summits.bed INFO @ Thu, 08 Oct 2020 19:50:52: Done! INFO @ Thu, 08 Oct 2020 19:50:54: 20000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:51:01: 21000000 INFO @ Thu, 08 Oct 2020 19:51:07: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:51:07: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:51:07: #1 total tags in treatment: 21829554 INFO @ Thu, 08 Oct 2020 19:51:07: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:51:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:51:07: #1 tags after filtering in treatment: 21829554 INFO @ Thu, 08 Oct 2020 19:51:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:51:07: #1 finished! INFO @ Thu, 08 Oct 2020 19:51:07: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:51:08: #2 number of paired peaks: 425 WARNING @ Thu, 08 Oct 2020 19:51:08: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Thu, 08 Oct 2020 19:51:08: start model_add_line... INFO @ Thu, 08 Oct 2020 19:51:09: start X-correlation... INFO @ Thu, 08 Oct 2020 19:51:09: end of X-cor INFO @ Thu, 08 Oct 2020 19:51:09: #2 finished! INFO @ Thu, 08 Oct 2020 19:51:09: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:51:09: #2 alternative fragment length(s) may be 1,17,42 bps INFO @ Thu, 08 Oct 2020 19:51:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.20_model.r WARNING @ Thu, 08 Oct 2020 19:51:09: #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, 08 Oct 2020 19:51:09: #2 You may need to consider one of the other alternative d(s): 1,17,42 WARNING @ Thu, 08 Oct 2020 19:51:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:51:09: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:51:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:51:16: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.10_summits.bed INFO @ Thu, 08 Oct 2020 19:51:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:51:41: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799192/SRX6799192.20_summits.bed INFO @ Thu, 08 Oct 2020 19:51:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling