Job ID = 14159259 SRX = SRX3180809 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11942106 spots for SRR6030460/SRR6030460.sra Written 11942106 spots for SRR6030460/SRR6030460.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159457 ("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: 00:02:53 11942106 reads; of these: 11942106 (100.00%) were unpaired; of these: 660249 (5.53%) aligned 0 times 9272282 (77.64%) aligned exactly 1 time 2009575 (16.83%) aligned >1 times 94.47% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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 8 files... [bam_rmdupse_core] 4542224 / 11281857 = 0.4026 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 20:37:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.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 20:37:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:37:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:37:20: 1000000 INFO @ Wed, 08 Dec 2021 20:37:25: 2000000 INFO @ Wed, 08 Dec 2021 20:37:31: 3000000 INFO @ Wed, 08 Dec 2021 20:37:36: 4000000 INFO @ Wed, 08 Dec 2021 20:37:41: 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 20:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.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 20:37:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:37:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:37:47: 6000000 INFO @ Wed, 08 Dec 2021 20:37:51: 1000000 INFO @ Wed, 08 Dec 2021 20:37:51: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:37:51: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:37:51: #1 total tags in treatment: 6739633 INFO @ Wed, 08 Dec 2021 20:37:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:37:51: #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 20:37:51: #1 tags after filtering in treatment: 6739633 INFO @ Wed, 08 Dec 2021 20:37:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:37:51: #1 finished! INFO @ Wed, 08 Dec 2021 20:37:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:37:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:37:51: #2 number of paired peaks: 509 WARNING @ Wed, 08 Dec 2021 20:37:51: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Wed, 08 Dec 2021 20:37:51: start model_add_line... INFO @ Wed, 08 Dec 2021 20:37:52: start X-correlation... INFO @ Wed, 08 Dec 2021 20:37:52: end of X-cor INFO @ Wed, 08 Dec 2021 20:37:52: #2 finished! INFO @ Wed, 08 Dec 2021 20:37:52: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 20:37:52: #2 alternative fragment length(s) may be 3,49,528,557 bps INFO @ Wed, 08 Dec 2021 20:37:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.05_model.r WARNING @ Wed, 08 Dec 2021 20:37:52: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:37:52: #2 You may need to consider one of the other alternative d(s): 3,49,528,557 WARNING @ Wed, 08 Dec 2021 20:37:52: #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 20:37:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:37:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:37:56: 2000000 INFO @ Wed, 08 Dec 2021 20:38:02: 3000000 INFO @ Wed, 08 Dec 2021 20:38:05: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:38:07: 4000000 INFO @ Wed, 08 Dec 2021 20:38:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:38:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:38:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.05_summits.bed INFO @ Wed, 08 Dec 2021 20:38:12: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (659 records, 4 fields): 211 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:38:13: 5000000 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 20:38:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.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 20:38:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:38:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:38:19: 6000000 INFO @ Wed, 08 Dec 2021 20:38:21: 1000000 INFO @ Wed, 08 Dec 2021 20:38:23: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:38:23: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:38:23: #1 total tags in treatment: 6739633 INFO @ Wed, 08 Dec 2021 20:38:23: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:38:23: #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 20:38:23: #1 tags after filtering in treatment: 6739633 INFO @ Wed, 08 Dec 2021 20:38:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:38:23: #1 finished! INFO @ Wed, 08 Dec 2021 20:38:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:38:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:38:24: #2 number of paired peaks: 509 WARNING @ Wed, 08 Dec 2021 20:38:24: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Wed, 08 Dec 2021 20:38:24: start model_add_line... INFO @ Wed, 08 Dec 2021 20:38:24: start X-correlation... INFO @ Wed, 08 Dec 2021 20:38:24: end of X-cor INFO @ Wed, 08 Dec 2021 20:38:24: #2 finished! INFO @ Wed, 08 Dec 2021 20:38:24: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 20:38:24: #2 alternative fragment length(s) may be 3,49,528,557 bps INFO @ Wed, 08 Dec 2021 20:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.10_model.r WARNING @ Wed, 08 Dec 2021 20:38:24: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:38:24: #2 You may need to consider one of the other alternative d(s): 3,49,528,557 WARNING @ Wed, 08 Dec 2021 20:38:24: #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 20:38:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:38:27: 2000000 INFO @ Wed, 08 Dec 2021 20:38:32: 3000000 INFO @ Wed, 08 Dec 2021 20:38:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:38:38: 4000000 INFO @ Wed, 08 Dec 2021 20:38:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:38:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:38:43: 5000000 INFO @ Wed, 08 Dec 2021 20:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.10_summits.bed INFO @ Wed, 08 Dec 2021 20:38:44: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (446 records, 4 fields): 91 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:38:49: 6000000 INFO @ Wed, 08 Dec 2021 20:38:53: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:38:53: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:38:53: #1 total tags in treatment: 6739633 INFO @ Wed, 08 Dec 2021 20:38:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:38:53: #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 20:38:53: #1 tags after filtering in treatment: 6739633 INFO @ Wed, 08 Dec 2021 20:38:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 20:38:53: #1 finished! INFO @ Wed, 08 Dec 2021 20:38:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:38:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:38:54: #2 number of paired peaks: 509 WARNING @ Wed, 08 Dec 2021 20:38:54: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Wed, 08 Dec 2021 20:38:54: start model_add_line... INFO @ Wed, 08 Dec 2021 20:38:54: start X-correlation... INFO @ Wed, 08 Dec 2021 20:38:54: end of X-cor INFO @ Wed, 08 Dec 2021 20:38:54: #2 finished! INFO @ Wed, 08 Dec 2021 20:38:54: #2 predicted fragment length is 49 bps INFO @ Wed, 08 Dec 2021 20:38:54: #2 alternative fragment length(s) may be 3,49,528,557 bps INFO @ Wed, 08 Dec 2021 20:38:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.20_model.r WARNING @ Wed, 08 Dec 2021 20:38:54: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:38:54: #2 You may need to consider one of the other alternative d(s): 3,49,528,557 WARNING @ Wed, 08 Dec 2021 20:38:54: #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 20:38:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:38:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:39:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:39:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180809/SRX3180809.20_summits.bed INFO @ Wed, 08 Dec 2021 20:39:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (200 records, 4 fields): 21 millis CompletedMACS2peakCalling