Job ID = 14160349 SRX = SRX9567173 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20321940 spots for SRR13125148/SRR13125148.sra Written 20321940 spots for SRR13125148/SRR13125148.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160611 ("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: 01:10:30 20321940 reads; of these: 20321940 (100.00%) were paired; of these: 7513525 (36.97%) aligned concordantly 0 times 6662447 (32.78%) aligned concordantly exactly 1 time 6145968 (30.24%) aligned concordantly >1 times ---- 7513525 pairs aligned concordantly 0 times; of these: 5159196 (68.67%) aligned discordantly 1 time ---- 2354329 pairs aligned 0 times concordantly or discordantly; of these: 4708658 mates make up the pairs; of these: 1941102 (41.22%) aligned 0 times 1238504 (26.30%) aligned exactly 1 time 1529052 (32.47%) aligned >1 times 95.22% overall alignment rate Time searching: 01:10:30 Overall time: 01:10:30 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 32 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] 12452458 / 17942760 = 0.6940 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 03:01:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.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 03:01:07: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:01:07: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:01:14: 1000000 INFO @ Thu, 09 Dec 2021 03:01:21: 2000000 INFO @ Thu, 09 Dec 2021 03:01:28: 3000000 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 03:01:35: 4000000 INFO @ Thu, 09 Dec 2021 03:01:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.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 03:01:37: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:01:37: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:01:43: 5000000 INFO @ Thu, 09 Dec 2021 03:01:47: 1000000 INFO @ Thu, 09 Dec 2021 03:01:52: 6000000 INFO @ Thu, 09 Dec 2021 03:01:57: 2000000 INFO @ Thu, 09 Dec 2021 03:02:00: 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 03:02:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.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 03:02:07: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:02:07: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:02:07: 3000000 INFO @ Thu, 09 Dec 2021 03:02:09: 8000000 INFO @ Thu, 09 Dec 2021 03:02:15: 1000000 INFO @ Thu, 09 Dec 2021 03:02:17: 4000000 INFO @ Thu, 09 Dec 2021 03:02:18: 9000000 INFO @ Thu, 09 Dec 2021 03:02:24: 2000000 INFO @ Thu, 09 Dec 2021 03:02:26: 10000000 INFO @ Thu, 09 Dec 2021 03:02:28: 5000000 INFO @ Thu, 09 Dec 2021 03:02:33: 3000000 INFO @ Thu, 09 Dec 2021 03:02:35: 11000000 INFO @ Thu, 09 Dec 2021 03:02:38: 6000000 INFO @ Thu, 09 Dec 2021 03:02:41: 4000000 INFO @ Thu, 09 Dec 2021 03:02:44: 12000000 INFO @ Thu, 09 Dec 2021 03:02:48: 7000000 INFO @ Thu, 09 Dec 2021 03:02:50: 5000000 INFO @ Thu, 09 Dec 2021 03:02:52: 13000000 INFO @ Thu, 09 Dec 2021 03:02:58: 8000000 INFO @ Thu, 09 Dec 2021 03:02:59: 6000000 INFO @ Thu, 09 Dec 2021 03:02:59: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:02:59: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:02:59: #1 total tags in treatment: 3933095 INFO @ Thu, 09 Dec 2021 03:02:59: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:02:59: #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 03:02:59: #1 tags after filtering in treatment: 2525245 INFO @ Thu, 09 Dec 2021 03:02:59: #1 Redundant rate of treatment: 0.36 INFO @ Thu, 09 Dec 2021 03:02:59: #1 finished! INFO @ Thu, 09 Dec 2021 03:02:59: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:02:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:02:59: #2 number of paired peaks: 1114 INFO @ Thu, 09 Dec 2021 03:02:59: start model_add_line... INFO @ Thu, 09 Dec 2021 03:02:59: start X-correlation... INFO @ Thu, 09 Dec 2021 03:02:59: end of X-cor INFO @ Thu, 09 Dec 2021 03:02:59: #2 finished! INFO @ Thu, 09 Dec 2021 03:02:59: #2 predicted fragment length is 302 bps INFO @ Thu, 09 Dec 2021 03:02:59: #2 alternative fragment length(s) may be 302 bps INFO @ Thu, 09 Dec 2021 03:02:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.05_model.r WARNING @ Thu, 09 Dec 2021 03:02:59: #2 Since the d (302) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:02:59: #2 You may need to consider one of the other alternative d(s): 302 WARNING @ Thu, 09 Dec 2021 03:02:59: #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 03:02:59: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:02:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:03:07: 7000000 INFO @ Thu, 09 Dec 2021 03:03:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:03:08: 9000000 INFO @ Thu, 09 Dec 2021 03:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.05_summits.bed INFO @ Thu, 09 Dec 2021 03:03:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (751 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:03:15: 8000000 INFO @ Thu, 09 Dec 2021 03:03:19: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:03:24: 9000000 INFO @ Thu, 09 Dec 2021 03:03:29: 11000000 INFO @ Thu, 09 Dec 2021 03:03:33: 10000000 INFO @ Thu, 09 Dec 2021 03:03:39: 12000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:03:41: 11000000 INFO @ Thu, 09 Dec 2021 03:03:49: 13000000 INFO @ Thu, 09 Dec 2021 03:03:49: 12000000 INFO @ Thu, 09 Dec 2021 03:03:56: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:03:56: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:03:56: #1 total tags in treatment: 3933095 INFO @ Thu, 09 Dec 2021 03:03:56: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:03:56: #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 03:03:56: #1 tags after filtering in treatment: 2525245 INFO @ Thu, 09 Dec 2021 03:03:56: #1 Redundant rate of treatment: 0.36 INFO @ Thu, 09 Dec 2021 03:03:56: #1 finished! INFO @ Thu, 09 Dec 2021 03:03:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:03:57: #2 number of paired peaks: 1114 INFO @ Thu, 09 Dec 2021 03:03:57: start model_add_line... INFO @ Thu, 09 Dec 2021 03:03:57: start X-correlation... INFO @ Thu, 09 Dec 2021 03:03:57: end of X-cor INFO @ Thu, 09 Dec 2021 03:03:57: #2 finished! INFO @ Thu, 09 Dec 2021 03:03:57: #2 predicted fragment length is 302 bps INFO @ Thu, 09 Dec 2021 03:03:57: #2 alternative fragment length(s) may be 302 bps INFO @ Thu, 09 Dec 2021 03:03:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.10_model.r WARNING @ Thu, 09 Dec 2021 03:03:57: #2 Since the d (302) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:03:57: #2 You may need to consider one of the other alternative d(s): 302 WARNING @ Thu, 09 Dec 2021 03:03:57: #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 03:03:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:03:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:03:57: 13000000 INFO @ Thu, 09 Dec 2021 03:04:03: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:04:03: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:04:03: #1 total tags in treatment: 3933095 INFO @ Thu, 09 Dec 2021 03:04:03: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:04:03: #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 03:04:04: #1 tags after filtering in treatment: 2525245 INFO @ Thu, 09 Dec 2021 03:04:04: #1 Redundant rate of treatment: 0.36 INFO @ Thu, 09 Dec 2021 03:04:04: #1 finished! INFO @ Thu, 09 Dec 2021 03:04:04: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:04:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:04:04: #2 number of paired peaks: 1114 INFO @ Thu, 09 Dec 2021 03:04:04: start model_add_line... INFO @ Thu, 09 Dec 2021 03:04:04: start X-correlation... INFO @ Thu, 09 Dec 2021 03:04:04: end of X-cor INFO @ Thu, 09 Dec 2021 03:04:04: #2 finished! INFO @ Thu, 09 Dec 2021 03:04:04: #2 predicted fragment length is 302 bps INFO @ Thu, 09 Dec 2021 03:04:04: #2 alternative fragment length(s) may be 302 bps INFO @ Thu, 09 Dec 2021 03:04:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.20_model.r WARNING @ Thu, 09 Dec 2021 03:04:04: #2 Since the d (302) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:04:04: #2 You may need to consider one of the other alternative d(s): 302 WARNING @ Thu, 09 Dec 2021 03:04:04: #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 03:04:04: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:04:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:04:05: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:04:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:04:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:04:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.10_summits.bed INFO @ Thu, 09 Dec 2021 03:04:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (593 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:04:13: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:04:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:04:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:04:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567173/SRX9567173.20_summits.bed INFO @ Thu, 09 Dec 2021 03:04:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (460 records, 4 fields): 2 millis CompletedMACS2peakCalling