Job ID = 14160302 SRX = SRX9567200 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8574763 spots for SRR13125175/SRR13125175.sra Written 8574763 spots for SRR13125175/SRR13125175.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160451 ("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: 00:16:39 8574763 reads; of these: 8574763 (100.00%) were paired; of these: 3586202 (41.82%) aligned concordantly 0 times 4312182 (50.29%) aligned concordantly exactly 1 time 676379 (7.89%) aligned concordantly >1 times ---- 3586202 pairs aligned concordantly 0 times; of these: 2408077 (67.15%) aligned discordantly 1 time ---- 1178125 pairs aligned 0 times concordantly or discordantly; of these: 2356250 mates make up the pairs; of these: 1284158 (54.50%) aligned 0 times 499879 (21.22%) aligned exactly 1 time 572213 (24.28%) aligned >1 times 92.51% overall alignment rate Time searching: 00:16:39 Overall time: 00:16:39 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] 6414019 / 7393300 = 0.8675 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 01:40:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.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 01:40:14: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:40:14: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:40:22: 1000000 INFO @ Thu, 09 Dec 2021 01:40:31: 2000000 INFO @ Thu, 09 Dec 2021 01:40:39: 3000000 INFO @ Thu, 09 Dec 2021 01:40:39: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 01:40:39: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 01:40:39: #1 total tags in treatment: 680955 INFO @ Thu, 09 Dec 2021 01:40:39: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:40:39: #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 01:40:39: #1 tags after filtering in treatment: 632688 INFO @ Thu, 09 Dec 2021 01:40:39: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 09 Dec 2021 01:40:39: #1 finished! INFO @ Thu, 09 Dec 2021 01:40:39: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:40:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:40:39: #2 number of paired peaks: 1414 INFO @ Thu, 09 Dec 2021 01:40:39: start model_add_line... INFO @ Thu, 09 Dec 2021 01:40:39: start X-correlation... INFO @ Thu, 09 Dec 2021 01:40:39: end of X-cor INFO @ Thu, 09 Dec 2021 01:40:39: #2 finished! INFO @ Thu, 09 Dec 2021 01:40:39: #2 predicted fragment length is 233 bps INFO @ Thu, 09 Dec 2021 01:40:39: #2 alternative fragment length(s) may be 233 bps INFO @ Thu, 09 Dec 2021 01:40:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.05_model.r WARNING @ Thu, 09 Dec 2021 01:40:39: #2 Since the d (233) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:40:39: #2 You may need to consider one of the other alternative d(s): 233 WARNING @ Thu, 09 Dec 2021 01:40:39: #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 01:40:39: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:40:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:40:41: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:40:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:40:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:40:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.05_summits.bed INFO @ Thu, 09 Dec 2021 01:40:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (355 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 01:40:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.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 01:40:44: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:40:44: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:40:52: 1000000 INFO @ Thu, 09 Dec 2021 01:41:00: 2000000 INFO @ Thu, 09 Dec 2021 01:41:09: 3000000 INFO @ Thu, 09 Dec 2021 01:41:09: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 01:41:09: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 01:41:09: #1 total tags in treatment: 680955 INFO @ Thu, 09 Dec 2021 01:41:09: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:41:09: #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 01:41:09: #1 tags after filtering in treatment: 632688 INFO @ Thu, 09 Dec 2021 01:41:09: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 09 Dec 2021 01:41:09: #1 finished! INFO @ Thu, 09 Dec 2021 01:41:09: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:41:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:41:09: #2 number of paired peaks: 1414 INFO @ Thu, 09 Dec 2021 01:41:09: start model_add_line... INFO @ Thu, 09 Dec 2021 01:41:09: start X-correlation... INFO @ Thu, 09 Dec 2021 01:41:09: end of X-cor INFO @ Thu, 09 Dec 2021 01:41:09: #2 finished! INFO @ Thu, 09 Dec 2021 01:41:09: #2 predicted fragment length is 233 bps INFO @ Thu, 09 Dec 2021 01:41:09: #2 alternative fragment length(s) may be 233 bps INFO @ Thu, 09 Dec 2021 01:41:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.10_model.r WARNING @ Thu, 09 Dec 2021 01:41:09: #2 Since the d (233) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:41:09: #2 You may need to consider one of the other alternative d(s): 233 WARNING @ Thu, 09 Dec 2021 01:41:09: #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 01:41:09: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:41:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:41:11: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:41:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:41:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:41:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.10_summits.bed INFO @ Thu, 09 Dec 2021 01:41:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (241 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 01:41:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.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 01:41:14: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:41:14: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:41:21: 1000000 INFO @ Thu, 09 Dec 2021 01:41:28: 2000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:41:35: 3000000 INFO @ Thu, 09 Dec 2021 01:41:35: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 01:41:35: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 01:41:35: #1 total tags in treatment: 680955 INFO @ Thu, 09 Dec 2021 01:41:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:41:35: #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 01:41:35: #1 tags after filtering in treatment: 632688 INFO @ Thu, 09 Dec 2021 01:41:35: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 09 Dec 2021 01:41:35: #1 finished! INFO @ Thu, 09 Dec 2021 01:41:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:41:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:41:35: #2 number of paired peaks: 1414 INFO @ Thu, 09 Dec 2021 01:41:35: start model_add_line... INFO @ Thu, 09 Dec 2021 01:41:35: start X-correlation... INFO @ Thu, 09 Dec 2021 01:41:35: end of X-cor INFO @ Thu, 09 Dec 2021 01:41:35: #2 finished! INFO @ Thu, 09 Dec 2021 01:41:35: #2 predicted fragment length is 233 bps INFO @ Thu, 09 Dec 2021 01:41:35: #2 alternative fragment length(s) may be 233 bps INFO @ Thu, 09 Dec 2021 01:41:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.20_model.r WARNING @ Thu, 09 Dec 2021 01:41:35: #2 Since the d (233) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:41:35: #2 You may need to consider one of the other alternative d(s): 233 WARNING @ Thu, 09 Dec 2021 01:41:35: #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 01:41:35: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:41:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:41:37: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:41:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:41:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:41:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567200/SRX9567200.20_summits.bed INFO @ Thu, 09 Dec 2021 01:41:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (131 records, 4 fields): 1 millis CompletedMACS2peakCalling