Job ID = 10165789 SRX = SRX9120619 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25413202 spots for SRR12638562/SRR12638562.sra Written 25413202 spots for SRR12638562/SRR12638562.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166104 ("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: 00:05:29 25413202 reads; of these: 25413202 (100.00%) were unpaired; of these: 1413575 (5.56%) aligned 0 times 20008967 (78.73%) aligned exactly 1 time 3990660 (15.70%) aligned >1 times 94.44% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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 12 files... [bam_rmdupse_core] 3479652 / 23999627 = 0.1450 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 20:03:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.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 20:03:59: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:03:59: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:04:04: 1000000 INFO @ Thu, 08 Oct 2020 20:04:10: 2000000 INFO @ Thu, 08 Oct 2020 20:04:15: 3000000 INFO @ Thu, 08 Oct 2020 20:04:21: 4000000 INFO @ Thu, 08 Oct 2020 20:04:26: 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, 08 Oct 2020 20:04:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.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 20:04:29: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:29: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:04:32: 6000000 INFO @ Thu, 08 Oct 2020 20:04:35: 1000000 INFO @ Thu, 08 Oct 2020 20:04:38: 7000000 INFO @ Thu, 08 Oct 2020 20:04:41: 2000000 INFO @ Thu, 08 Oct 2020 20:04:44: 8000000 INFO @ Thu, 08 Oct 2020 20:04:47: 3000000 INFO @ Thu, 08 Oct 2020 20:04:50: 9000000 INFO @ Thu, 08 Oct 2020 20:04:53: 4000000 INFO @ Thu, 08 Oct 2020 20:04:56: 10000000 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 20:04:59: 5000000 INFO @ Thu, 08 Oct 2020 20:04:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.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 20:04:59: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:59: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:05:02: 11000000 INFO @ Thu, 08 Oct 2020 20:05:05: 6000000 INFO @ Thu, 08 Oct 2020 20:05:05: 1000000 INFO @ Thu, 08 Oct 2020 20:05:08: 12000000 INFO @ Thu, 08 Oct 2020 20:05:11: 2000000 INFO @ Thu, 08 Oct 2020 20:05:11: 7000000 INFO @ Thu, 08 Oct 2020 20:05:14: 13000000 INFO @ Thu, 08 Oct 2020 20:05:17: 8000000 INFO @ Thu, 08 Oct 2020 20:05:17: 3000000 INFO @ Thu, 08 Oct 2020 20:05:20: 14000000 INFO @ Thu, 08 Oct 2020 20:05:23: 9000000 INFO @ Thu, 08 Oct 2020 20:05:23: 4000000 INFO @ Thu, 08 Oct 2020 20:05:26: 15000000 INFO @ Thu, 08 Oct 2020 20:05:29: 10000000 INFO @ Thu, 08 Oct 2020 20:05:29: 5000000 INFO @ Thu, 08 Oct 2020 20:05:32: 16000000 INFO @ Thu, 08 Oct 2020 20:05:35: 11000000 INFO @ Thu, 08 Oct 2020 20:05:35: 6000000 INFO @ Thu, 08 Oct 2020 20:05:38: 17000000 INFO @ Thu, 08 Oct 2020 20:05:41: 12000000 INFO @ Thu, 08 Oct 2020 20:05:41: 7000000 INFO @ Thu, 08 Oct 2020 20:05:44: 18000000 INFO @ Thu, 08 Oct 2020 20:05:47: 13000000 INFO @ Thu, 08 Oct 2020 20:05:47: 8000000 INFO @ Thu, 08 Oct 2020 20:05:50: 19000000 INFO @ Thu, 08 Oct 2020 20:05:52: 14000000 INFO @ Thu, 08 Oct 2020 20:05:53: 9000000 INFO @ Thu, 08 Oct 2020 20:05:56: 20000000 INFO @ Thu, 08 Oct 2020 20:05:58: 15000000 INFO @ Thu, 08 Oct 2020 20:05:59: 10000000 INFO @ Thu, 08 Oct 2020 20:05:59: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:05:59: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:05:59: #1 total tags in treatment: 20519975 INFO @ Thu, 08 Oct 2020 20:05:59: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:05:59: #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 20:06:00: #1 tags after filtering in treatment: 20519975 INFO @ Thu, 08 Oct 2020 20:06:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:00: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:00: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:01: #2 number of paired peaks: 176 WARNING @ Thu, 08 Oct 2020 20:06:01: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:01: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:01: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:01: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:01: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:01: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:06:01: #2 alternative fragment length(s) may be 0,14,46,586 bps INFO @ Thu, 08 Oct 2020 20:06:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.05_model.r WARNING @ Thu, 08 Oct 2020 20:06:01: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:06:01: #2 You may need to consider one of the other alternative d(s): 0,14,46,586 WARNING @ Thu, 08 Oct 2020 20:06:01: #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 20:06:01: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:04: 16000000 INFO @ Thu, 08 Oct 2020 20:06:04: 11000000 INFO @ Thu, 08 Oct 2020 20:06:07: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:06:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:06:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:06:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.05_summits.bed INFO @ Thu, 08 Oct 2020 20:06:07: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:06:10: 12000000 INFO @ Thu, 08 Oct 2020 20:06:10: 17000000 INFO @ Thu, 08 Oct 2020 20:06:16: 13000000 INFO @ Thu, 08 Oct 2020 20:06:16: 18000000 INFO @ Thu, 08 Oct 2020 20:06:22: 14000000 INFO @ Thu, 08 Oct 2020 20:06:22: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:06:27: 15000000 INFO @ Thu, 08 Oct 2020 20:06:28: 20000000 INFO @ Thu, 08 Oct 2020 20:06:31: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:31: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:31: #1 total tags in treatment: 20519975 INFO @ Thu, 08 Oct 2020 20:06:31: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:31: #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 20:06:31: #1 tags after filtering in treatment: 20519975 INFO @ Thu, 08 Oct 2020 20:06:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:31: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:31: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:32: #2 number of paired peaks: 176 WARNING @ Thu, 08 Oct 2020 20:06:32: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:32: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:33: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:33: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:33: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:33: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:06:33: #2 alternative fragment length(s) may be 0,14,46,586 bps INFO @ Thu, 08 Oct 2020 20:06:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.10_model.r WARNING @ Thu, 08 Oct 2020 20:06:33: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:06:33: #2 You may need to consider one of the other alternative d(s): 0,14,46,586 WARNING @ Thu, 08 Oct 2020 20:06:33: #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 20:06:33: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:33: 16000000 INFO @ Thu, 08 Oct 2020 20:06:38: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:06:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:06:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:06:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.10_summits.bed INFO @ Thu, 08 Oct 2020 20:06:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:06:39: 17000000 INFO @ Thu, 08 Oct 2020 20:06:44: 18000000 INFO @ Thu, 08 Oct 2020 20:06:49: 19000000 INFO @ Thu, 08 Oct 2020 20:06:54: 20000000 INFO @ Thu, 08 Oct 2020 20:06:57: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:57: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:57: #1 total tags in treatment: 20519975 INFO @ Thu, 08 Oct 2020 20:06:57: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:57: #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 20:06:57: #1 tags after filtering in treatment: 20519975 INFO @ Thu, 08 Oct 2020 20:06:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:57: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:57: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:59: #2 number of paired peaks: 176 WARNING @ Thu, 08 Oct 2020 20:06:59: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:59: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:59: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:59: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:59: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:59: #2 predicted fragment length is 0 bps INFO @ Thu, 08 Oct 2020 20:06:59: #2 alternative fragment length(s) may be 0,14,46,586 bps INFO @ Thu, 08 Oct 2020 20:06:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.20_model.r WARNING @ Thu, 08 Oct 2020 20:06:59: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:06:59: #2 You may need to consider one of the other alternative d(s): 0,14,46,586 WARNING @ Thu, 08 Oct 2020 20:06:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:06:59: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:07:04: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120619/SRX9120619.20_summits.bed INFO @ Thu, 08 Oct 2020 20:07:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。