Job ID = 14160420 SRX = SRX9567199 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13328720 spots for SRR13125174/SRR13125174.sra Written 13328720 spots for SRR13125174/SRR13125174.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160606 ("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: 00:25:30 13328720 reads; of these: 13328720 (100.00%) were paired; of these: 6695734 (50.24%) aligned concordantly 0 times 5931165 (44.50%) aligned concordantly exactly 1 time 701821 (5.27%) aligned concordantly >1 times ---- 6695734 pairs aligned concordantly 0 times; of these: 5190201 (77.52%) aligned discordantly 1 time ---- 1505533 pairs aligned 0 times concordantly or discordantly; of these: 3011066 mates make up the pairs; of these: 892516 (29.64%) aligned 0 times 987742 (32.80%) aligned exactly 1 time 1130808 (37.56%) aligned >1 times 96.65% overall alignment rate Time searching: 00:25:30 Overall time: 00:25:30 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 20 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] 7969943 / 11818158 = 0.6744 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 @ Thu, 09 Dec 2021 02:53:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.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 @ Thu, 09 Dec 2021 02:53:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:53:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:53:22: 1000000 INFO @ Thu, 09 Dec 2021 02:53:28: 2000000 INFO @ Thu, 09 Dec 2021 02:53:35: 3000000 INFO @ Thu, 09 Dec 2021 02:53:42: 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 @ Thu, 09 Dec 2021 02:53:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.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 @ Thu, 09 Dec 2021 02:53:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:53:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:53:49: 5000000 INFO @ Thu, 09 Dec 2021 02:53:54: 1000000 INFO @ Thu, 09 Dec 2021 02:53:57: 6000000 INFO @ Thu, 09 Dec 2021 02:54:04: 2000000 INFO @ Thu, 09 Dec 2021 02:54:05: 7000000 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 @ Thu, 09 Dec 2021 02:54:13: 8000000 INFO @ Thu, 09 Dec 2021 02:54:13: 3000000 INFO @ Thu, 09 Dec 2021 02:54:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.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 @ Thu, 09 Dec 2021 02:54:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:54:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:54:21: 9000000 INFO @ Thu, 09 Dec 2021 02:54:23: 1000000 INFO @ Thu, 09 Dec 2021 02:54:23: 4000000 INFO @ Thu, 09 Dec 2021 02:54:28: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:54:28: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:54:28: #1 total tags in treatment: 2162218 INFO @ Thu, 09 Dec 2021 02:54:28: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:54:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:54:28: #1 tags after filtering in treatment: 2054003 INFO @ Thu, 09 Dec 2021 02:54:28: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 02:54:28: #1 finished! INFO @ Thu, 09 Dec 2021 02:54:28: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:54:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:54:28: #2 number of paired peaks: 2423 INFO @ Thu, 09 Dec 2021 02:54:28: start model_add_line... INFO @ Thu, 09 Dec 2021 02:54:28: start X-correlation... INFO @ Thu, 09 Dec 2021 02:54:28: end of X-cor INFO @ Thu, 09 Dec 2021 02:54:28: #2 finished! INFO @ Thu, 09 Dec 2021 02:54:28: #2 predicted fragment length is 291 bps INFO @ Thu, 09 Dec 2021 02:54:28: #2 alternative fragment length(s) may be 291 bps INFO @ Thu, 09 Dec 2021 02:54:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.05_model.r WARNING @ Thu, 09 Dec 2021 02:54:28: #2 Since the d (291) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:54:28: #2 You may need to consider one of the other alternative d(s): 291 WARNING @ Thu, 09 Dec 2021 02:54:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:54:28: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:54:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:54:31: 2000000 INFO @ Thu, 09 Dec 2021 02:54:33: 5000000 INFO @ Thu, 09 Dec 2021 02:54:33: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:54:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:54:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:54:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.05_summits.bed INFO @ Thu, 09 Dec 2021 02:54:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1678 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:54:39: 3000000 INFO @ Thu, 09 Dec 2021 02:54:42: 6000000 INFO @ Thu, 09 Dec 2021 02:54:47: 4000000 INFO @ Thu, 09 Dec 2021 02:54:52: 7000000 INFO @ Thu, 09 Dec 2021 02:54:55: 5000000 INFO @ Thu, 09 Dec 2021 02:55:01: 8000000 INFO @ Thu, 09 Dec 2021 02:55:03: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:55:10: 9000000 INFO @ Thu, 09 Dec 2021 02:55:11: 7000000 INFO @ Thu, 09 Dec 2021 02:55:18: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:55:18: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:55:18: #1 total tags in treatment: 2162218 INFO @ Thu, 09 Dec 2021 02:55:18: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:55:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:55:18: #1 tags after filtering in treatment: 2054003 INFO @ Thu, 09 Dec 2021 02:55:18: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 02:55:18: #1 finished! INFO @ Thu, 09 Dec 2021 02:55:18: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:55:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:55:18: #2 number of paired peaks: 2423 INFO @ Thu, 09 Dec 2021 02:55:18: start model_add_line... INFO @ Thu, 09 Dec 2021 02:55:18: start X-correlation... INFO @ Thu, 09 Dec 2021 02:55:18: end of X-cor INFO @ Thu, 09 Dec 2021 02:55:18: #2 finished! INFO @ Thu, 09 Dec 2021 02:55:18: #2 predicted fragment length is 291 bps INFO @ Thu, 09 Dec 2021 02:55:18: #2 alternative fragment length(s) may be 291 bps INFO @ Thu, 09 Dec 2021 02:55:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.10_model.r WARNING @ Thu, 09 Dec 2021 02:55:18: #2 Since the d (291) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:55:18: #2 You may need to consider one of the other alternative d(s): 291 WARNING @ Thu, 09 Dec 2021 02:55:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:55:18: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:55:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:55:19: 8000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:55:23: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:55:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:55:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:55:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.10_summits.bed INFO @ Thu, 09 Dec 2021 02:55:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (800 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:55:26: 9000000 INFO @ Thu, 09 Dec 2021 02:55:32: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:55:32: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:55:32: #1 total tags in treatment: 2162218 INFO @ Thu, 09 Dec 2021 02:55:32: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:55:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:55:32: #1 tags after filtering in treatment: 2054003 INFO @ Thu, 09 Dec 2021 02:55:32: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 02:55:32: #1 finished! INFO @ Thu, 09 Dec 2021 02:55:32: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:55:32: #2 number of paired peaks: 2423 INFO @ Thu, 09 Dec 2021 02:55:32: start model_add_line... INFO @ Thu, 09 Dec 2021 02:55:32: start X-correlation... INFO @ Thu, 09 Dec 2021 02:55:32: end of X-cor INFO @ Thu, 09 Dec 2021 02:55:32: #2 finished! INFO @ Thu, 09 Dec 2021 02:55:32: #2 predicted fragment length is 291 bps INFO @ Thu, 09 Dec 2021 02:55:32: #2 alternative fragment length(s) may be 291 bps INFO @ Thu, 09 Dec 2021 02:55:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.20_model.r WARNING @ Thu, 09 Dec 2021 02:55:32: #2 Since the d (291) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:55:32: #2 You may need to consider one of the other alternative d(s): 291 WARNING @ Thu, 09 Dec 2021 02:55:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:55:32: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:55:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:55:37: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:55:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:55:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:55:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567199/SRX9567199.20_summits.bed INFO @ Thu, 09 Dec 2021 02:55:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (357 records, 4 fields): 1 millis CompletedMACS2peakCalling