Job ID = 14159615 SRX = SRX3180781 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8410553 spots for SRR6030432/SRR6030432.sra Written 8410553 spots for SRR6030432/SRR6030432.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160113 ("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: 00:02:19 8410553 reads; of these: 8410553 (100.00%) were unpaired; of these: 839909 (9.99%) aligned 0 times 6316082 (75.10%) aligned exactly 1 time 1254562 (14.92%) aligned >1 times 90.01% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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_rmdupse_core] 1985840 / 7570644 = 0.2623 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 23:27:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.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 23:27:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:27:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:27:38: 1000000 INFO @ Wed, 08 Dec 2021 23:27:47: 2000000 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 23:27:55: 3000000 INFO @ Wed, 08 Dec 2021 23:27:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.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 23:27:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:27:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:28:05: 1000000 INFO @ Wed, 08 Dec 2021 23:28:05: 4000000 INFO @ Wed, 08 Dec 2021 23:28:12: 2000000 INFO @ Wed, 08 Dec 2021 23:28:14: 5000000 INFO @ Wed, 08 Dec 2021 23:28:18: 3000000 INFO @ Wed, 08 Dec 2021 23:28:19: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:28:19: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:28:19: #1 total tags in treatment: 5584804 INFO @ Wed, 08 Dec 2021 23:28:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:28:19: #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 23:28:20: #1 tags after filtering in treatment: 5584804 INFO @ Wed, 08 Dec 2021 23:28:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:28:20: #1 finished! INFO @ Wed, 08 Dec 2021 23:28:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:28:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:28:20: #2 number of paired peaks: 451 WARNING @ Wed, 08 Dec 2021 23:28:20: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Wed, 08 Dec 2021 23:28:20: start model_add_line... INFO @ Wed, 08 Dec 2021 23:28:20: start X-correlation... INFO @ Wed, 08 Dec 2021 23:28:20: end of X-cor INFO @ Wed, 08 Dec 2021 23:28:20: #2 finished! INFO @ Wed, 08 Dec 2021 23:28:20: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 23:28:20: #2 alternative fragment length(s) may be 4,50,506,523 bps INFO @ Wed, 08 Dec 2021 23:28:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.05_model.r WARNING @ Wed, 08 Dec 2021 23:28:20: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:28:20: #2 You may need to consider one of the other alternative d(s): 4,50,506,523 WARNING @ Wed, 08 Dec 2021 23:28:20: #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 23:28:20: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:28:20: #3 Pre-compute pvalue-qvalue table... 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 23:28:26: 4000000 INFO @ Wed, 08 Dec 2021 23:28:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.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 23:28:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:28:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:28:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:28:34: 5000000 INFO @ Wed, 08 Dec 2021 23:28:38: 1000000 INFO @ Wed, 08 Dec 2021 23:28:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:28:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:28:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.05_summits.bed INFO @ Wed, 08 Dec 2021 23:28:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (583 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:28:40: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:28:40: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:28:40: #1 total tags in treatment: 5584804 INFO @ Wed, 08 Dec 2021 23:28:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:28:40: #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 23:28:40: #1 tags after filtering in treatment: 5584804 INFO @ Wed, 08 Dec 2021 23:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:28:40: #1 finished! INFO @ Wed, 08 Dec 2021 23:28:40: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:28:40: #2 number of paired peaks: 451 WARNING @ Wed, 08 Dec 2021 23:28:40: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Wed, 08 Dec 2021 23:28:40: start model_add_line... INFO @ Wed, 08 Dec 2021 23:28:40: start X-correlation... INFO @ Wed, 08 Dec 2021 23:28:40: end of X-cor INFO @ Wed, 08 Dec 2021 23:28:40: #2 finished! INFO @ Wed, 08 Dec 2021 23:28:40: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 23:28:40: #2 alternative fragment length(s) may be 4,50,506,523 bps INFO @ Wed, 08 Dec 2021 23:28:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.10_model.r WARNING @ Wed, 08 Dec 2021 23:28:40: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:28:40: #2 You may need to consider one of the other alternative d(s): 4,50,506,523 WARNING @ Wed, 08 Dec 2021 23:28:40: #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 23:28:40: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:28:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:28:47: 2000000 INFO @ Wed, 08 Dec 2021 23:28:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:28:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:28:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:28:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.10_summits.bed INFO @ Wed, 08 Dec 2021 23:28:57: Done! INFO @ Wed, 08 Dec 2021 23:28:57: 3000000 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (385 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:29:07: 4000000 INFO @ Wed, 08 Dec 2021 23:29:16: 5000000 INFO @ Wed, 08 Dec 2021 23:29:22: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:29:22: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:29:22: #1 total tags in treatment: 5584804 INFO @ Wed, 08 Dec 2021 23:29:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:29:22: #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 23:29:22: #1 tags after filtering in treatment: 5584804 INFO @ Wed, 08 Dec 2021 23:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:29:22: #1 finished! INFO @ Wed, 08 Dec 2021 23:29:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:29:23: #2 number of paired peaks: 451 WARNING @ Wed, 08 Dec 2021 23:29:23: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Wed, 08 Dec 2021 23:29:23: start model_add_line... INFO @ Wed, 08 Dec 2021 23:29:23: start X-correlation... INFO @ Wed, 08 Dec 2021 23:29:23: end of X-cor INFO @ Wed, 08 Dec 2021 23:29:23: #2 finished! INFO @ Wed, 08 Dec 2021 23:29:23: #2 predicted fragment length is 50 bps INFO @ Wed, 08 Dec 2021 23:29:23: #2 alternative fragment length(s) may be 4,50,506,523 bps INFO @ Wed, 08 Dec 2021 23:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.20_model.r WARNING @ Wed, 08 Dec 2021 23:29:23: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:29:23: #2 You may need to consider one of the other alternative d(s): 4,50,506,523 WARNING @ Wed, 08 Dec 2021 23:29:23: #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 23:29:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:29:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:29:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:29:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:29:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:29:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180781/SRX3180781.20_summits.bed INFO @ Wed, 08 Dec 2021 23:29:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (151 records, 4 fields): 1 millis CompletedMACS2peakCalling