Job ID = 16432879 SRX = SRX13336901 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30550362 spots for SRR17152887/SRR17152887.sra Written 30550362 spots for SRR17152887/SRR17152887.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434835 ("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: 00:18:36 30550362 reads; of these: 30550362 (100.00%) were paired; of these: 26586505 (87.03%) aligned concordantly 0 times 3347681 (10.96%) aligned concordantly exactly 1 time 616176 (2.02%) aligned concordantly >1 times ---- 26586505 pairs aligned concordantly 0 times; of these: 2054840 (7.73%) aligned discordantly 1 time ---- 24531665 pairs aligned 0 times concordantly or discordantly; of these: 49063330 mates make up the pairs; of these: 48195886 (98.23%) aligned 0 times 447172 (0.91%) aligned exactly 1 time 420272 (0.86%) aligned >1 times 21.12% overall alignment rate Time searching: 00:18:36 Overall time: 00:18:36 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1018769 / 6005778 = 0.1696 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:01:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.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 @ Tue, 02 Aug 2022 10:01:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:01:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:01:48: 1000000 INFO @ Tue, 02 Aug 2022 10:01:56: 2000000 INFO @ Tue, 02 Aug 2022 10:02:05: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:02:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.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 @ Tue, 02 Aug 2022 10:02:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:02:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:02:13: 4000000 INFO @ Tue, 02 Aug 2022 10:02:18: 1000000 INFO @ Tue, 02 Aug 2022 10:02:22: 5000000 INFO @ Tue, 02 Aug 2022 10:02:25: 2000000 INFO @ Tue, 02 Aug 2022 10:02:31: 6000000 INFO @ Tue, 02 Aug 2022 10:02:33: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:02:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.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 @ Tue, 02 Aug 2022 10:02:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:02:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:02:40: 7000000 INFO @ Tue, 02 Aug 2022 10:02:41: 4000000 INFO @ Tue, 02 Aug 2022 10:02:48: 1000000 INFO @ Tue, 02 Aug 2022 10:02:48: 8000000 INFO @ Tue, 02 Aug 2022 10:02:49: 5000000 INFO @ Tue, 02 Aug 2022 10:02:56: 2000000 INFO @ Tue, 02 Aug 2022 10:02:57: 9000000 INFO @ Tue, 02 Aug 2022 10:02:57: 6000000 INFO @ Tue, 02 Aug 2022 10:03:04: 3000000 INFO @ Tue, 02 Aug 2022 10:03:05: 7000000 INFO @ Tue, 02 Aug 2022 10:03:06: 10000000 INFO @ Tue, 02 Aug 2022 10:03:12: 4000000 INFO @ Tue, 02 Aug 2022 10:03:13: 8000000 INFO @ Tue, 02 Aug 2022 10:03:14: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 10:03:14: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 10:03:14: #1 total tags in treatment: 3247019 INFO @ Tue, 02 Aug 2022 10:03:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:03:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:03:14: #1 tags after filtering in treatment: 3094998 INFO @ Tue, 02 Aug 2022 10:03:14: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 10:03:14: #1 finished! INFO @ Tue, 02 Aug 2022 10:03:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:03:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:03:14: #2 number of paired peaks: 569 WARNING @ Tue, 02 Aug 2022 10:03:14: Fewer paired peaks (569) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 569 pairs to build model! INFO @ Tue, 02 Aug 2022 10:03:14: start model_add_line... INFO @ Tue, 02 Aug 2022 10:03:14: start X-correlation... INFO @ Tue, 02 Aug 2022 10:03:14: end of X-cor INFO @ Tue, 02 Aug 2022 10:03:14: #2 finished! INFO @ Tue, 02 Aug 2022 10:03:14: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 10:03:14: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 10:03:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.05_model.r WARNING @ Tue, 02 Aug 2022 10:03:14: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:03:14: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 10:03:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:03:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:03:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:03:20: 5000000 INFO @ Tue, 02 Aug 2022 10:03:20: 9000000 INFO @ Tue, 02 Aug 2022 10:03:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:03:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:03:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:03:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.05_summits.bed INFO @ Tue, 02 Aug 2022 10:03:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (615 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:03:27: 6000000 INFO @ Tue, 02 Aug 2022 10:03:28: 10000000 INFO @ Tue, 02 Aug 2022 10:03:34: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 10:03:34: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 10:03:34: #1 total tags in treatment: 3247019 INFO @ Tue, 02 Aug 2022 10:03:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:03:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:03:34: #1 tags after filtering in treatment: 3094998 INFO @ Tue, 02 Aug 2022 10:03:34: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 10:03:34: #1 finished! INFO @ Tue, 02 Aug 2022 10:03:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:03:34: #2 number of paired peaks: 569 WARNING @ Tue, 02 Aug 2022 10:03:34: Fewer paired peaks (569) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 569 pairs to build model! INFO @ Tue, 02 Aug 2022 10:03:34: start model_add_line... INFO @ Tue, 02 Aug 2022 10:03:34: start X-correlation... INFO @ Tue, 02 Aug 2022 10:03:34: end of X-cor INFO @ Tue, 02 Aug 2022 10:03:34: #2 finished! INFO @ Tue, 02 Aug 2022 10:03:34: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 10:03:34: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 10:03:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.10_model.r WARNING @ Tue, 02 Aug 2022 10:03:34: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:03:34: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 10:03:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:03:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:03:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:03:35: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:03:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:03:42: 8000000 INFO @ Tue, 02 Aug 2022 10:03:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:03:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:03:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.10_summits.bed INFO @ Tue, 02 Aug 2022 10:03:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (336 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:03:49: 9000000 INFO @ Tue, 02 Aug 2022 10:03:56: 10000000 INFO @ Tue, 02 Aug 2022 10:04:02: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 10:04:02: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 10:04:02: #1 total tags in treatment: 3247019 INFO @ Tue, 02 Aug 2022 10:04:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:04:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:04:02: #1 tags after filtering in treatment: 3094998 INFO @ Tue, 02 Aug 2022 10:04:02: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 10:04:02: #1 finished! INFO @ Tue, 02 Aug 2022 10:04:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:04:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:04:03: #2 number of paired peaks: 569 WARNING @ Tue, 02 Aug 2022 10:04:03: Fewer paired peaks (569) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 569 pairs to build model! INFO @ Tue, 02 Aug 2022 10:04:03: start model_add_line... INFO @ Tue, 02 Aug 2022 10:04:03: start X-correlation... INFO @ Tue, 02 Aug 2022 10:04:03: end of X-cor INFO @ Tue, 02 Aug 2022 10:04:03: #2 finished! INFO @ Tue, 02 Aug 2022 10:04:03: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 10:04:03: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 10:04:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.20_model.r WARNING @ Tue, 02 Aug 2022 10:04:03: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:04:03: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 10:04:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:04:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:04:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:04:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336901/SRX13336901.20_summits.bed INFO @ Tue, 02 Aug 2022 10:04:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 15 millis CompletedMACS2peakCalling