Job ID = 14157886 SRX = SRX10040017 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 45524033 spots for SRR13642804/SRR13642804.sra Written 45524033 spots for SRR13642804/SRR13642804.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158089 ("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: 00:09:17 45524033 reads; of these: 45524033 (100.00%) were unpaired; of these: 4277126 (9.40%) aligned 0 times 30310870 (66.58%) aligned exactly 1 time 10936037 (24.02%) aligned >1 times 90.60% overall alignment rate Time searching: 00:09:17 Overall time: 00:09:17 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_rmdupse_core] 11581949 / 41246907 = 0.2808 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 12:35:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.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, 08 Dec 2021 12:35:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:35:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:35:36: 1000000 INFO @ Wed, 08 Dec 2021 12:35:42: 2000000 INFO @ Wed, 08 Dec 2021 12:35:47: 3000000 INFO @ Wed, 08 Dec 2021 12:35:53: 4000000 INFO @ Wed, 08 Dec 2021 12:35:58: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 12:36:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.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, 08 Dec 2021 12:36:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:36:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:36:05: 6000000 INFO @ Wed, 08 Dec 2021 12:36:08: 1000000 INFO @ Wed, 08 Dec 2021 12:36:12: 7000000 INFO @ Wed, 08 Dec 2021 12:36:16: 2000000 INFO @ Wed, 08 Dec 2021 12:36:18: 8000000 INFO @ Wed, 08 Dec 2021 12:36:24: 3000000 INFO @ Wed, 08 Dec 2021 12:36:25: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 12:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.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, 08 Dec 2021 12:36:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:36:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:36:31: 4000000 INFO @ Wed, 08 Dec 2021 12:36:32: 10000000 INFO @ Wed, 08 Dec 2021 12:36:38: 1000000 INFO @ Wed, 08 Dec 2021 12:36:39: 5000000 INFO @ Wed, 08 Dec 2021 12:36:39: 11000000 INFO @ Wed, 08 Dec 2021 12:36:44: 2000000 INFO @ Wed, 08 Dec 2021 12:36:46: 12000000 INFO @ Wed, 08 Dec 2021 12:36:46: 6000000 INFO @ Wed, 08 Dec 2021 12:36:51: 3000000 INFO @ Wed, 08 Dec 2021 12:36:53: 13000000 INFO @ Wed, 08 Dec 2021 12:36:54: 7000000 INFO @ Wed, 08 Dec 2021 12:36:58: 4000000 INFO @ Wed, 08 Dec 2021 12:37:00: 14000000 INFO @ Wed, 08 Dec 2021 12:37:02: 8000000 INFO @ Wed, 08 Dec 2021 12:37:05: 5000000 INFO @ Wed, 08 Dec 2021 12:37:06: 15000000 INFO @ Wed, 08 Dec 2021 12:37:09: 9000000 INFO @ Wed, 08 Dec 2021 12:37:12: 6000000 INFO @ Wed, 08 Dec 2021 12:37:13: 16000000 INFO @ Wed, 08 Dec 2021 12:37:17: 10000000 INFO @ Wed, 08 Dec 2021 12:37:18: 7000000 INFO @ Wed, 08 Dec 2021 12:37:20: 17000000 INFO @ Wed, 08 Dec 2021 12:37:24: 11000000 INFO @ Wed, 08 Dec 2021 12:37:25: 8000000 INFO @ Wed, 08 Dec 2021 12:37:27: 18000000 INFO @ Wed, 08 Dec 2021 12:37:32: 12000000 INFO @ Wed, 08 Dec 2021 12:37:32: 9000000 INFO @ Wed, 08 Dec 2021 12:37:34: 19000000 INFO @ Wed, 08 Dec 2021 12:37:39: 10000000 INFO @ Wed, 08 Dec 2021 12:37:40: 13000000 INFO @ Wed, 08 Dec 2021 12:37:41: 20000000 INFO @ Wed, 08 Dec 2021 12:37:46: 11000000 INFO @ Wed, 08 Dec 2021 12:37:47: 14000000 INFO @ Wed, 08 Dec 2021 12:37:48: 21000000 INFO @ Wed, 08 Dec 2021 12:37:52: 12000000 INFO @ Wed, 08 Dec 2021 12:37:55: 22000000 INFO @ Wed, 08 Dec 2021 12:37:55: 15000000 INFO @ Wed, 08 Dec 2021 12:37:59: 13000000 INFO @ Wed, 08 Dec 2021 12:38:01: 23000000 INFO @ Wed, 08 Dec 2021 12:38:03: 16000000 INFO @ Wed, 08 Dec 2021 12:38:06: 14000000 INFO @ Wed, 08 Dec 2021 12:38:08: 24000000 INFO @ Wed, 08 Dec 2021 12:38:10: 17000000 INFO @ Wed, 08 Dec 2021 12:38:13: 15000000 INFO @ Wed, 08 Dec 2021 12:38:15: 25000000 INFO @ Wed, 08 Dec 2021 12:38:18: 18000000 INFO @ Wed, 08 Dec 2021 12:38:20: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:38:22: 26000000 INFO @ Wed, 08 Dec 2021 12:38:25: 19000000 INFO @ Wed, 08 Dec 2021 12:38:27: 17000000 INFO @ Wed, 08 Dec 2021 12:38:29: 27000000 INFO @ Wed, 08 Dec 2021 12:38:33: 20000000 INFO @ Wed, 08 Dec 2021 12:38:34: 18000000 INFO @ Wed, 08 Dec 2021 12:38:36: 28000000 INFO @ Wed, 08 Dec 2021 12:38:41: 19000000 INFO @ Wed, 08 Dec 2021 12:38:41: 21000000 INFO @ Wed, 08 Dec 2021 12:38:43: 29000000 INFO @ Wed, 08 Dec 2021 12:38:47: 20000000 INFO @ Wed, 08 Dec 2021 12:38:47: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 12:38:47: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 12:38:47: #1 total tags in treatment: 29664958 INFO @ Wed, 08 Dec 2021 12:38:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:38:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:38:48: #1 tags after filtering in treatment: 29664958 INFO @ Wed, 08 Dec 2021 12:38:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:38:48: #1 finished! INFO @ Wed, 08 Dec 2021 12:38:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:38:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:38:48: 22000000 INFO @ Wed, 08 Dec 2021 12:38:50: #2 number of paired peaks: 193 WARNING @ Wed, 08 Dec 2021 12:38:50: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Wed, 08 Dec 2021 12:38:50: start model_add_line... INFO @ Wed, 08 Dec 2021 12:38:50: start X-correlation... INFO @ Wed, 08 Dec 2021 12:38:50: end of X-cor INFO @ Wed, 08 Dec 2021 12:38:50: #2 finished! INFO @ Wed, 08 Dec 2021 12:38:50: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 12:38:50: #2 alternative fragment length(s) may be 1,36,115 bps INFO @ Wed, 08 Dec 2021 12:38:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.05_model.r WARNING @ Wed, 08 Dec 2021 12:38:50: #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, 08 Dec 2021 12:38:50: #2 You may need to consider one of the other alternative d(s): 1,36,115 WARNING @ Wed, 08 Dec 2021 12:38:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:38:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:38:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:38:54: 21000000 INFO @ Wed, 08 Dec 2021 12:38:56: 23000000 INFO @ Wed, 08 Dec 2021 12:39:01: 22000000 INFO @ Wed, 08 Dec 2021 12:39:03: 24000000 INFO @ Wed, 08 Dec 2021 12:39:07: 23000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:39:11: 25000000 INFO @ Wed, 08 Dec 2021 12:39:14: 24000000 INFO @ Wed, 08 Dec 2021 12:39:18: 26000000 INFO @ Wed, 08 Dec 2021 12:39:21: 25000000 INFO @ Wed, 08 Dec 2021 12:39:26: 27000000 INFO @ Wed, 08 Dec 2021 12:39:26: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:39:27: 26000000 INFO @ Wed, 08 Dec 2021 12:39:34: 28000000 INFO @ Wed, 08 Dec 2021 12:39:34: 27000000 INFO @ Wed, 08 Dec 2021 12:39:41: 28000000 INFO @ Wed, 08 Dec 2021 12:39:41: 29000000 INFO @ Wed, 08 Dec 2021 12:39:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:39:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:39:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.05_summits.bed INFO @ Wed, 08 Dec 2021 12:39:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:39:46: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 12:39:46: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 12:39:46: #1 total tags in treatment: 29664958 INFO @ Wed, 08 Dec 2021 12:39:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:39:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:39:47: #1 tags after filtering in treatment: 29664958 INFO @ Wed, 08 Dec 2021 12:39:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:39:47: #1 finished! INFO @ Wed, 08 Dec 2021 12:39:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:39:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:39:47: 29000000 INFO @ Wed, 08 Dec 2021 12:39:49: #2 number of paired peaks: 193 WARNING @ Wed, 08 Dec 2021 12:39:49: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Wed, 08 Dec 2021 12:39:49: start model_add_line... INFO @ Wed, 08 Dec 2021 12:39:49: start X-correlation... INFO @ Wed, 08 Dec 2021 12:39:49: end of X-cor INFO @ Wed, 08 Dec 2021 12:39:49: #2 finished! INFO @ Wed, 08 Dec 2021 12:39:49: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 12:39:49: #2 alternative fragment length(s) may be 1,36,115 bps INFO @ Wed, 08 Dec 2021 12:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.10_model.r WARNING @ Wed, 08 Dec 2021 12:39:49: #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, 08 Dec 2021 12:39:49: #2 You may need to consider one of the other alternative d(s): 1,36,115 WARNING @ Wed, 08 Dec 2021 12:39:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:39:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:39:52: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 12:39:52: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 12:39:52: #1 total tags in treatment: 29664958 INFO @ Wed, 08 Dec 2021 12:39:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:39:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:39:52: #1 tags after filtering in treatment: 29664958 INFO @ Wed, 08 Dec 2021 12:39:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:39:52: #1 finished! INFO @ Wed, 08 Dec 2021 12:39:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:39:54: #2 number of paired peaks: 193 WARNING @ Wed, 08 Dec 2021 12:39:54: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Wed, 08 Dec 2021 12:39:54: start model_add_line... INFO @ Wed, 08 Dec 2021 12:39:54: start X-correlation... INFO @ Wed, 08 Dec 2021 12:39:54: end of X-cor INFO @ Wed, 08 Dec 2021 12:39:54: #2 finished! INFO @ Wed, 08 Dec 2021 12:39:54: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 12:39:54: #2 alternative fragment length(s) may be 1,36,115 bps INFO @ Wed, 08 Dec 2021 12:39:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.20_model.r WARNING @ Wed, 08 Dec 2021 12:39:54: #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, 08 Dec 2021 12:39:54: #2 You may need to consider one of the other alternative d(s): 1,36,115 WARNING @ Wed, 08 Dec 2021 12:39:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:39:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:40:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:40:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:40:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:40:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:40:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.10_summits.bed INFO @ Wed, 08 Dec 2021 12:40:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:40:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:40:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:40:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040017/SRX10040017.20_summits.bed INFO @ Wed, 08 Dec 2021 12:40:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling