Job ID = 14160419 SRX = SRX9567198 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14224263 spots for SRR13125173/SRR13125173.sra Written 14224263 spots for SRR13125173/SRR13125173.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160634 ("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: 00:36:21 14224263 reads; of these: 14224263 (100.00%) were paired; of these: 5486356 (38.57%) aligned concordantly 0 times 7840529 (55.12%) aligned concordantly exactly 1 time 897378 (6.31%) aligned concordantly >1 times ---- 5486356 pairs aligned concordantly 0 times; of these: 4113350 (74.97%) aligned discordantly 1 time ---- 1373006 pairs aligned 0 times concordantly or discordantly; of these: 2746012 mates make up the pairs; of these: 1039778 (37.87%) aligned 0 times 790841 (28.80%) aligned exactly 1 time 915393 (33.34%) aligned >1 times 96.35% overall alignment rate Time searching: 00:36:21 Overall time: 00:36:21 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] 9819121 / 12846739 = 0.7643 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 03:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.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 03:07:32: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:32: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:45: 1000000 INFO @ Thu, 09 Dec 2021 03:07:57: 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 @ Thu, 09 Dec 2021 03:08:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.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 03:08:02: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:08:02: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:08:09: 3000000 INFO @ Thu, 09 Dec 2021 03:08:17: 1000000 INFO @ Thu, 09 Dec 2021 03:08:22: 4000000 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 03:08:31: 2000000 INFO @ Thu, 09 Dec 2021 03:08:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.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 03:08:31: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:08:31: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:08:36: 5000000 INFO @ Thu, 09 Dec 2021 03:08:45: 3000000 INFO @ Thu, 09 Dec 2021 03:08:46: 1000000 INFO @ Thu, 09 Dec 2021 03:08:52: 6000000 INFO @ Thu, 09 Dec 2021 03:09:00: 2000000 INFO @ Thu, 09 Dec 2021 03:09:00: 4000000 INFO @ Thu, 09 Dec 2021 03:09:07: 7000000 INFO @ Thu, 09 Dec 2021 03:09:15: 3000000 INFO @ Thu, 09 Dec 2021 03:09:16: 5000000 INFO @ Thu, 09 Dec 2021 03:09:19: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:09:19: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:09:19: #1 total tags in treatment: 2063545 INFO @ Thu, 09 Dec 2021 03:09:19: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:09:19: #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 03:09:19: #1 tags after filtering in treatment: 1952499 INFO @ Thu, 09 Dec 2021 03:09:19: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 03:09:19: #1 finished! INFO @ Thu, 09 Dec 2021 03:09:19: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:09:19: #2 number of paired peaks: 2070 INFO @ Thu, 09 Dec 2021 03:09:19: start model_add_line... INFO @ Thu, 09 Dec 2021 03:09:19: start X-correlation... INFO @ Thu, 09 Dec 2021 03:09:19: end of X-cor INFO @ Thu, 09 Dec 2021 03:09:19: #2 finished! INFO @ Thu, 09 Dec 2021 03:09:19: #2 predicted fragment length is 276 bps INFO @ Thu, 09 Dec 2021 03:09:19: #2 alternative fragment length(s) may be 276 bps INFO @ Thu, 09 Dec 2021 03:09:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.05_model.r WARNING @ Thu, 09 Dec 2021 03:09:19: #2 Since the d (276) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:09:19: #2 You may need to consider one of the other alternative d(s): 276 WARNING @ Thu, 09 Dec 2021 03:09:19: #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 03:09:19: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:09:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:09:25: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:09:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:09:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:09:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.05_summits.bed INFO @ Thu, 09 Dec 2021 03:09:28: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1553 records, 4 fields): 34 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:09:30: 6000000 INFO @ Thu, 09 Dec 2021 03:09:30: 4000000 INFO @ Thu, 09 Dec 2021 03:09:44: 7000000 INFO @ Thu, 09 Dec 2021 03:09:44: 5000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:09:55: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:09:55: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:09:55: #1 total tags in treatment: 2063545 INFO @ Thu, 09 Dec 2021 03:09:55: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:09:55: #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 03:09:55: #1 tags after filtering in treatment: 1952499 INFO @ Thu, 09 Dec 2021 03:09:55: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 03:09:55: #1 finished! INFO @ Thu, 09 Dec 2021 03:09:55: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:09:55: #2 number of paired peaks: 2070 INFO @ Thu, 09 Dec 2021 03:09:55: start model_add_line... INFO @ Thu, 09 Dec 2021 03:09:55: start X-correlation... INFO @ Thu, 09 Dec 2021 03:09:56: end of X-cor INFO @ Thu, 09 Dec 2021 03:09:56: #2 finished! INFO @ Thu, 09 Dec 2021 03:09:56: #2 predicted fragment length is 276 bps INFO @ Thu, 09 Dec 2021 03:09:56: #2 alternative fragment length(s) may be 276 bps INFO @ Thu, 09 Dec 2021 03:09:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.10_model.r WARNING @ Thu, 09 Dec 2021 03:09:56: #2 Since the d (276) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:09:56: #2 You may need to consider one of the other alternative d(s): 276 WARNING @ Thu, 09 Dec 2021 03:09:56: #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 03:09:56: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:09:58: 6000000 INFO @ Thu, 09 Dec 2021 03:10:01: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:10:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:10:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:10:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.10_summits.bed INFO @ Thu, 09 Dec 2021 03:10:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (702 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:10:12: 7000000 INFO @ Thu, 09 Dec 2021 03:10:22: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:10:22: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:10:22: #1 total tags in treatment: 2063545 INFO @ Thu, 09 Dec 2021 03:10:22: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:10:22: #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 03:10:22: #1 tags after filtering in treatment: 1952499 INFO @ Thu, 09 Dec 2021 03:10:22: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 03:10:22: #1 finished! INFO @ Thu, 09 Dec 2021 03:10:22: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:10:23: #2 number of paired peaks: 2070 INFO @ Thu, 09 Dec 2021 03:10:23: start model_add_line... INFO @ Thu, 09 Dec 2021 03:10:23: start X-correlation... INFO @ Thu, 09 Dec 2021 03:10:23: end of X-cor INFO @ Thu, 09 Dec 2021 03:10:23: #2 finished! INFO @ Thu, 09 Dec 2021 03:10:23: #2 predicted fragment length is 276 bps INFO @ Thu, 09 Dec 2021 03:10:23: #2 alternative fragment length(s) may be 276 bps INFO @ Thu, 09 Dec 2021 03:10:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.20_model.r WARNING @ Thu, 09 Dec 2021 03:10:23: #2 Since the d (276) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:10:23: #2 You may need to consider one of the other alternative d(s): 276 WARNING @ Thu, 09 Dec 2021 03:10:23: #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 03:10:23: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:10:29: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:10:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:10:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:10:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567198/SRX9567198.20_summits.bed INFO @ Thu, 09 Dec 2021 03:10:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (341 records, 4 fields): 1 millis CompletedMACS2peakCalling