Job ID = 14157875 SRX = SRX6799193 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 37378121 spots for SRR10065400/SRR10065400.sra Written 37378121 spots for SRR10065400/SRR10065400.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158054 ("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: 00:08:08 37378121 reads; of these: 37378121 (100.00%) were unpaired; of these: 1962851 (5.25%) aligned 0 times 25265945 (67.60%) aligned exactly 1 time 10149325 (27.15%) aligned >1 times 94.75% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 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] 11215970 / 35415270 = 0.3167 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 12:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.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 12:10:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:10:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:11:00: 1000000 INFO @ Wed, 08 Dec 2021 12:11:05: 2000000 INFO @ Wed, 08 Dec 2021 12:11:10: 3000000 INFO @ Wed, 08 Dec 2021 12:11:15: 4000000 INFO @ Wed, 08 Dec 2021 12:11:20: 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 12:11:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.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 12:11:25: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:11:25: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:11:25: 6000000 INFO @ Wed, 08 Dec 2021 12:11:30: 7000000 INFO @ Wed, 08 Dec 2021 12:11:31: 1000000 INFO @ Wed, 08 Dec 2021 12:11:36: 8000000 INFO @ Wed, 08 Dec 2021 12:11:37: 2000000 INFO @ Wed, 08 Dec 2021 12:11:41: 9000000 INFO @ Wed, 08 Dec 2021 12:11:43: 3000000 INFO @ Wed, 08 Dec 2021 12:11:46: 10000000 INFO @ Wed, 08 Dec 2021 12:11:48: 4000000 INFO @ Wed, 08 Dec 2021 12:11:51: 11000000 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 12:11:54: 5000000 INFO @ Wed, 08 Dec 2021 12:11:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.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 12:11:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:11:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:11:57: 12000000 INFO @ Wed, 08 Dec 2021 12:12:00: 6000000 INFO @ Wed, 08 Dec 2021 12:12:00: 1000000 INFO @ Wed, 08 Dec 2021 12:12:02: 13000000 INFO @ Wed, 08 Dec 2021 12:12:05: 2000000 INFO @ Wed, 08 Dec 2021 12:12:06: 7000000 INFO @ Wed, 08 Dec 2021 12:12:07: 14000000 INFO @ Wed, 08 Dec 2021 12:12:10: 3000000 INFO @ Wed, 08 Dec 2021 12:12:11: 8000000 INFO @ Wed, 08 Dec 2021 12:12:12: 15000000 INFO @ Wed, 08 Dec 2021 12:12:15: 4000000 INFO @ Wed, 08 Dec 2021 12:12:17: 9000000 INFO @ Wed, 08 Dec 2021 12:12:18: 16000000 INFO @ Wed, 08 Dec 2021 12:12:20: 5000000 INFO @ Wed, 08 Dec 2021 12:12:23: 17000000 INFO @ Wed, 08 Dec 2021 12:12:23: 10000000 INFO @ Wed, 08 Dec 2021 12:12:25: 6000000 INFO @ Wed, 08 Dec 2021 12:12:28: 18000000 INFO @ Wed, 08 Dec 2021 12:12:29: 11000000 INFO @ Wed, 08 Dec 2021 12:12:30: 7000000 INFO @ Wed, 08 Dec 2021 12:12:33: 19000000 INFO @ Wed, 08 Dec 2021 12:12:35: 12000000 INFO @ Wed, 08 Dec 2021 12:12:35: 8000000 INFO @ Wed, 08 Dec 2021 12:12:39: 20000000 INFO @ Wed, 08 Dec 2021 12:12:40: 9000000 INFO @ Wed, 08 Dec 2021 12:12:40: 13000000 INFO @ Wed, 08 Dec 2021 12:12:44: 21000000 INFO @ Wed, 08 Dec 2021 12:12:45: 10000000 INFO @ Wed, 08 Dec 2021 12:12:46: 14000000 INFO @ Wed, 08 Dec 2021 12:12:49: 22000000 INFO @ Wed, 08 Dec 2021 12:12:50: 11000000 INFO @ Wed, 08 Dec 2021 12:12:52: 15000000 INFO @ Wed, 08 Dec 2021 12:12:54: 23000000 INFO @ Wed, 08 Dec 2021 12:12:55: 12000000 INFO @ Wed, 08 Dec 2021 12:12:58: 16000000 INFO @ Wed, 08 Dec 2021 12:13:00: 24000000 INFO @ Wed, 08 Dec 2021 12:13:00: 13000000 INFO @ Wed, 08 Dec 2021 12:13:01: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:13:01: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:13:01: #1 total tags in treatment: 24199300 INFO @ Wed, 08 Dec 2021 12:13:01: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:13:01: #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 12:13:01: #1 tags after filtering in treatment: 24199300 INFO @ Wed, 08 Dec 2021 12:13:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:13:01: #1 finished! INFO @ Wed, 08 Dec 2021 12:13:01: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:13:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:13:03: #2 number of paired peaks: 318 WARNING @ Wed, 08 Dec 2021 12:13:03: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Wed, 08 Dec 2021 12:13:03: start model_add_line... INFO @ Wed, 08 Dec 2021 12:13:03: start X-correlation... INFO @ Wed, 08 Dec 2021 12:13:03: end of X-cor INFO @ Wed, 08 Dec 2021 12:13:03: #2 finished! INFO @ Wed, 08 Dec 2021 12:13:03: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 12:13:03: #2 alternative fragment length(s) may be 1,11 bps INFO @ Wed, 08 Dec 2021 12:13:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.05_model.r WARNING @ Wed, 08 Dec 2021 12:13:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:13:03: #2 You may need to consider one of the other alternative d(s): 1,11 WARNING @ Wed, 08 Dec 2021 12:13:03: #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 12:13:03: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:13:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:13:04: 17000000 INFO @ Wed, 08 Dec 2021 12:13:05: 14000000 INFO @ Wed, 08 Dec 2021 12:13:09: 18000000 INFO @ Wed, 08 Dec 2021 12:13:10: 15000000 INFO @ Wed, 08 Dec 2021 12:13:15: 19000000 INFO @ Wed, 08 Dec 2021 12:13:15: 16000000 INFO @ Wed, 08 Dec 2021 12:13:20: 17000000 INFO @ Wed, 08 Dec 2021 12:13:21: 20000000 INFO @ Wed, 08 Dec 2021 12:13:25: 18000000 INFO @ Wed, 08 Dec 2021 12:13:26: 21000000 INFO @ Wed, 08 Dec 2021 12:13:30: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:13:32: 22000000 INFO @ Wed, 08 Dec 2021 12:13:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:13:35: 20000000 INFO @ Wed, 08 Dec 2021 12:13:38: 23000000 INFO @ Wed, 08 Dec 2021 12:13:40: 21000000 INFO @ Wed, 08 Dec 2021 12:13:44: 24000000 INFO @ Wed, 08 Dec 2021 12:13:45: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:13:45: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:13:45: #1 total tags in treatment: 24199300 INFO @ Wed, 08 Dec 2021 12:13:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:13:45: #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 12:13:45: 22000000 INFO @ Wed, 08 Dec 2021 12:13:45: #1 tags after filtering in treatment: 24199300 INFO @ Wed, 08 Dec 2021 12:13:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:13:45: #1 finished! INFO @ Wed, 08 Dec 2021 12:13:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:13:47: #2 number of paired peaks: 318 WARNING @ Wed, 08 Dec 2021 12:13:47: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Wed, 08 Dec 2021 12:13:47: start model_add_line... INFO @ Wed, 08 Dec 2021 12:13:47: start X-correlation... INFO @ Wed, 08 Dec 2021 12:13:47: end of X-cor INFO @ Wed, 08 Dec 2021 12:13:47: #2 finished! INFO @ Wed, 08 Dec 2021 12:13:47: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 12:13:47: #2 alternative fragment length(s) may be 1,11 bps INFO @ Wed, 08 Dec 2021 12:13:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.10_model.r WARNING @ Wed, 08 Dec 2021 12:13:47: #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 12:13:47: #2 You may need to consider one of the other alternative d(s): 1,11 WARNING @ Wed, 08 Dec 2021 12:13:47: #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 12:13:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:13:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:13:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:13:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:13:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.05_summits.bed INFO @ Wed, 08 Dec 2021 12:13:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:13:50: 23000000 INFO @ Wed, 08 Dec 2021 12:13:55: 24000000 INFO @ Wed, 08 Dec 2021 12:13:56: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:13:56: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:13:56: #1 total tags in treatment: 24199300 INFO @ Wed, 08 Dec 2021 12:13:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:13:56: #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 12:13:56: #1 tags after filtering in treatment: 24199300 INFO @ Wed, 08 Dec 2021 12:13:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:13:56: #1 finished! INFO @ Wed, 08 Dec 2021 12:13:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:13:58: #2 number of paired peaks: 318 WARNING @ Wed, 08 Dec 2021 12:13:58: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Wed, 08 Dec 2021 12:13:58: start model_add_line... INFO @ Wed, 08 Dec 2021 12:13:58: start X-correlation... INFO @ Wed, 08 Dec 2021 12:13:58: end of X-cor INFO @ Wed, 08 Dec 2021 12:13:58: #2 finished! INFO @ Wed, 08 Dec 2021 12:13:58: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 12:13:58: #2 alternative fragment length(s) may be 1,11 bps INFO @ Wed, 08 Dec 2021 12:13:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.20_model.r WARNING @ Wed, 08 Dec 2021 12:13:58: #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 12:13:58: #2 You may need to consider one of the other alternative d(s): 1,11 WARNING @ Wed, 08 Dec 2021 12:13:58: #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 12:13:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:13:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:14:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:14:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:14:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:14:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:14:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.10_summits.bed INFO @ Wed, 08 Dec 2021 12:14:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:14:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:14:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:14:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.20_summits.bed INFO @ Wed, 08 Dec 2021 12:14:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling