Job ID = 14159230 SRX = SRX9120621 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25118456 spots for SRR12638564/SRR12638564.sra Written 25118456 spots for SRR12638564/SRR12638564.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159440 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:24 25118456 reads; of these: 25118456 (100.00%) were unpaired; of these: 808601 (3.22%) aligned 0 times 20321755 (80.90%) aligned exactly 1 time 3988100 (15.88%) aligned >1 times 96.78% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 3713527 / 24309855 = 0.1528 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 20:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.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 20:30:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:30:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:30:10: 1000000 INFO @ Wed, 08 Dec 2021 20:30:15: 2000000 INFO @ Wed, 08 Dec 2021 20:30:21: 3000000 INFO @ Wed, 08 Dec 2021 20:30:26: 4000000 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 20:30:32: 5000000 INFO @ Wed, 08 Dec 2021 20:30:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.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 20:30:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:30:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:30:38: 6000000 INFO @ Wed, 08 Dec 2021 20:30:41: 1000000 INFO @ Wed, 08 Dec 2021 20:30:44: 7000000 INFO @ Wed, 08 Dec 2021 20:30:47: 2000000 INFO @ Wed, 08 Dec 2021 20:30:50: 8000000 INFO @ Wed, 08 Dec 2021 20:30:53: 3000000 INFO @ Wed, 08 Dec 2021 20:30:57: 9000000 INFO @ Wed, 08 Dec 2021 20:31:00: 4000000 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 20:31:03: 10000000 INFO @ Wed, 08 Dec 2021 20:31:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.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 20:31:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:31:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:31:06: 5000000 INFO @ Wed, 08 Dec 2021 20:31:10: 11000000 INFO @ Wed, 08 Dec 2021 20:31:11: 1000000 INFO @ Wed, 08 Dec 2021 20:31:13: 6000000 INFO @ Wed, 08 Dec 2021 20:31:17: 12000000 INFO @ Wed, 08 Dec 2021 20:31:17: 2000000 INFO @ Wed, 08 Dec 2021 20:31:20: 7000000 INFO @ Wed, 08 Dec 2021 20:31:24: 13000000 INFO @ Wed, 08 Dec 2021 20:31:24: 3000000 INFO @ Wed, 08 Dec 2021 20:31:26: 8000000 INFO @ Wed, 08 Dec 2021 20:31:30: 14000000 INFO @ Wed, 08 Dec 2021 20:31:31: 4000000 INFO @ Wed, 08 Dec 2021 20:31:33: 9000000 INFO @ Wed, 08 Dec 2021 20:31:37: 15000000 INFO @ Wed, 08 Dec 2021 20:31:38: 5000000 INFO @ Wed, 08 Dec 2021 20:31:40: 10000000 INFO @ Wed, 08 Dec 2021 20:31:44: 16000000 INFO @ Wed, 08 Dec 2021 20:31:45: 6000000 INFO @ Wed, 08 Dec 2021 20:31:47: 11000000 INFO @ Wed, 08 Dec 2021 20:31:51: 17000000 INFO @ Wed, 08 Dec 2021 20:31:51: 7000000 INFO @ Wed, 08 Dec 2021 20:31:53: 12000000 INFO @ Wed, 08 Dec 2021 20:31:57: 18000000 INFO @ Wed, 08 Dec 2021 20:31:58: 8000000 INFO @ Wed, 08 Dec 2021 20:32:00: 13000000 INFO @ Wed, 08 Dec 2021 20:32:04: 19000000 INFO @ Wed, 08 Dec 2021 20:32:05: 9000000 INFO @ Wed, 08 Dec 2021 20:32:07: 14000000 INFO @ Wed, 08 Dec 2021 20:32:11: 20000000 INFO @ Wed, 08 Dec 2021 20:32:11: 10000000 INFO @ Wed, 08 Dec 2021 20:32:13: 15000000 INFO @ Wed, 08 Dec 2021 20:32:15: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:32:15: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:32:15: #1 total tags in treatment: 20596328 INFO @ Wed, 08 Dec 2021 20:32:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:32:15: #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 20:32:15: #1 tags after filtering in treatment: 20596328 INFO @ Wed, 08 Dec 2021 20:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:32:15: #1 finished! INFO @ Wed, 08 Dec 2021 20:32:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:32:16: #2 number of paired peaks: 176 WARNING @ Wed, 08 Dec 2021 20:32:16: 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 @ Wed, 08 Dec 2021 20:32:16: start model_add_line... INFO @ Wed, 08 Dec 2021 20:32:17: start X-correlation... INFO @ Wed, 08 Dec 2021 20:32:17: end of X-cor INFO @ Wed, 08 Dec 2021 20:32:17: #2 finished! INFO @ Wed, 08 Dec 2021 20:32:17: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:32:17: #2 alternative fragment length(s) may be 1,47,532,554,582 bps INFO @ Wed, 08 Dec 2021 20:32:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.05_model.r WARNING @ Wed, 08 Dec 2021 20:32:17: #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 20:32:17: #2 You may need to consider one of the other alternative d(s): 1,47,532,554,582 WARNING @ Wed, 08 Dec 2021 20:32:17: #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 20:32:17: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:32:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:32:18: 11000000 INFO @ Wed, 08 Dec 2021 20:32:20: 16000000 INFO @ Wed, 08 Dec 2021 20:32:25: 12000000 INFO @ Wed, 08 Dec 2021 20:32:27: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:32:32: 13000000 INFO @ Wed, 08 Dec 2021 20:32:34: 18000000 INFO @ Wed, 08 Dec 2021 20:32:39: 14000000 INFO @ Wed, 08 Dec 2021 20:32:41: 19000000 INFO @ Wed, 08 Dec 2021 20:32:45: 15000000 INFO @ Wed, 08 Dec 2021 20:32:47: 20000000 INFO @ Wed, 08 Dec 2021 20:32:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:32:51: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:32:51: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:32:51: #1 total tags in treatment: 20596328 INFO @ Wed, 08 Dec 2021 20:32:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:32:51: #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 20:32:52: #1 tags after filtering in treatment: 20596328 INFO @ Wed, 08 Dec 2021 20:32:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:32:52: #1 finished! INFO @ Wed, 08 Dec 2021 20:32:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:32:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:32:52: 16000000 INFO @ Wed, 08 Dec 2021 20:32:53: #2 number of paired peaks: 176 WARNING @ Wed, 08 Dec 2021 20:32:53: 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 @ Wed, 08 Dec 2021 20:32:53: start model_add_line... INFO @ Wed, 08 Dec 2021 20:32:53: start X-correlation... INFO @ Wed, 08 Dec 2021 20:32:53: end of X-cor INFO @ Wed, 08 Dec 2021 20:32:53: #2 finished! INFO @ Wed, 08 Dec 2021 20:32:53: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:32:53: #2 alternative fragment length(s) may be 1,47,532,554,582 bps INFO @ Wed, 08 Dec 2021 20:32:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.10_model.r WARNING @ Wed, 08 Dec 2021 20:32:53: #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 20:32:53: #2 You may need to consider one of the other alternative d(s): 1,47,532,554,582 WARNING @ Wed, 08 Dec 2021 20:32:53: #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 20:32:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:32:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:32:59: 17000000 INFO @ Wed, 08 Dec 2021 20:33:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:33:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:33:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.05_summits.bed INFO @ Wed, 08 Dec 2021 20:33:02: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:33:05: 18000000 INFO @ Wed, 08 Dec 2021 20:33:11: 19000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:33:17: 20000000 INFO @ Wed, 08 Dec 2021 20:33:21: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 20:33:21: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 20:33:21: #1 total tags in treatment: 20596328 INFO @ Wed, 08 Dec 2021 20:33:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:33:21: #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 20:33:21: #1 tags after filtering in treatment: 20596328 INFO @ Wed, 08 Dec 2021 20:33:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:33:21: #1 finished! INFO @ Wed, 08 Dec 2021 20:33:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:33:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:33:23: #2 number of paired peaks: 176 WARNING @ Wed, 08 Dec 2021 20:33:23: 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 @ Wed, 08 Dec 2021 20:33:23: start model_add_line... INFO @ Wed, 08 Dec 2021 20:33:23: start X-correlation... INFO @ Wed, 08 Dec 2021 20:33:23: end of X-cor INFO @ Wed, 08 Dec 2021 20:33:23: #2 finished! INFO @ Wed, 08 Dec 2021 20:33:23: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 20:33:23: #2 alternative fragment length(s) may be 1,47,532,554,582 bps INFO @ Wed, 08 Dec 2021 20:33:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.20_model.r WARNING @ Wed, 08 Dec 2021 20:33:23: #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, 08 Dec 2021 20:33:23: #2 You may need to consider one of the other alternative d(s): 1,47,532,554,582 WARNING @ Wed, 08 Dec 2021 20:33:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:33:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:33:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:33:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:33:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:33:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.10_summits.bed INFO @ Wed, 08 Dec 2021 20:33:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:33:54: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:34:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:34:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:34:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120621/SRX9120621.20_summits.bed INFO @ Wed, 08 Dec 2021 20:34:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling