Job ID = 14159563 SRX = SRX8845650 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34629867 spots for SRR12345957/SRR12345957.sra Written 34629867 spots for SRR12345957/SRR12345957.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159941 ("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: 00:24:15 34629867 reads; of these: 34629867 (100.00%) were paired; of these: 17615724 (50.87%) aligned concordantly 0 times 14547715 (42.01%) aligned concordantly exactly 1 time 2466428 (7.12%) aligned concordantly >1 times ---- 17615724 pairs aligned concordantly 0 times; of these: 3701995 (21.02%) aligned discordantly 1 time ---- 13913729 pairs aligned 0 times concordantly or discordantly; of these: 27827458 mates make up the pairs; of these: 25103541 (90.21%) aligned 0 times 1275198 (4.58%) aligned exactly 1 time 1448719 (5.21%) aligned >1 times 63.75% overall alignment rate Time searching: 00:24:15 Overall time: 00:24:15 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] 19074758 / 20485313 = 0.9311 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 @ Wed, 08 Dec 2021 23:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.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 @ Wed, 08 Dec 2021 23:07:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:07:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:07:45: 1000000 INFO @ Wed, 08 Dec 2021 23:07:51: 2000000 INFO @ Wed, 08 Dec 2021 23:07:57: 3000000 INFO @ Wed, 08 Dec 2021 23:08:03: 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 @ Wed, 08 Dec 2021 23:08:08: 5000000 INFO @ Wed, 08 Dec 2021 23:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.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 @ Wed, 08 Dec 2021 23:08:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:08:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:08:15: 6000000 INFO @ Wed, 08 Dec 2021 23:08:15: #1 tag size is determined as 73 bps INFO @ Wed, 08 Dec 2021 23:08:15: #1 tag size = 73 INFO @ Wed, 08 Dec 2021 23:08:15: #1 total tags in treatment: 1123287 INFO @ Wed, 08 Dec 2021 23:08:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:08:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:08:15: #1 tags after filtering in treatment: 662424 INFO @ Wed, 08 Dec 2021 23:08:15: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 08 Dec 2021 23:08:15: #1 finished! INFO @ Wed, 08 Dec 2021 23:08:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:08:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:08:15: #2 number of paired peaks: 4367 INFO @ Wed, 08 Dec 2021 23:08:15: start model_add_line... INFO @ Wed, 08 Dec 2021 23:08:16: start X-correlation... INFO @ Wed, 08 Dec 2021 23:08:16: end of X-cor INFO @ Wed, 08 Dec 2021 23:08:16: #2 finished! INFO @ Wed, 08 Dec 2021 23:08:16: #2 predicted fragment length is 114 bps INFO @ Wed, 08 Dec 2021 23:08:16: #2 alternative fragment length(s) may be 114 bps INFO @ Wed, 08 Dec 2021 23:08:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.05_model.r WARNING @ Wed, 08 Dec 2021 23:08:16: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:08:16: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Wed, 08 Dec 2021 23:08:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:08:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:08:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:08:17: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:08:17: 1000000 INFO @ Wed, 08 Dec 2021 23:08:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:08:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:08:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.05_summits.bed INFO @ Wed, 08 Dec 2021 23:08:18: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3279 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:08:25: 2000000 INFO @ Wed, 08 Dec 2021 23:08:33: 3000000 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 @ Wed, 08 Dec 2021 23:08:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.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 @ Wed, 08 Dec 2021 23:08:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:08:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:08:40: 4000000 INFO @ Wed, 08 Dec 2021 23:08:47: 1000000 INFO @ Wed, 08 Dec 2021 23:08:49: 5000000 INFO @ Wed, 08 Dec 2021 23:08:54: 2000000 INFO @ Wed, 08 Dec 2021 23:08:57: 6000000 INFO @ Wed, 08 Dec 2021 23:08:57: #1 tag size is determined as 73 bps INFO @ Wed, 08 Dec 2021 23:08:57: #1 tag size = 73 INFO @ Wed, 08 Dec 2021 23:08:57: #1 total tags in treatment: 1123287 INFO @ Wed, 08 Dec 2021 23:08:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:08:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:08:57: #1 tags after filtering in treatment: 662424 INFO @ Wed, 08 Dec 2021 23:08:57: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 08 Dec 2021 23:08:57: #1 finished! INFO @ Wed, 08 Dec 2021 23:08:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:08:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:08:57: #2 number of paired peaks: 4367 INFO @ Wed, 08 Dec 2021 23:08:57: start model_add_line... INFO @ Wed, 08 Dec 2021 23:08:57: start X-correlation... INFO @ Wed, 08 Dec 2021 23:08:57: end of X-cor INFO @ Wed, 08 Dec 2021 23:08:57: #2 finished! INFO @ Wed, 08 Dec 2021 23:08:57: #2 predicted fragment length is 114 bps INFO @ Wed, 08 Dec 2021 23:08:57: #2 alternative fragment length(s) may be 114 bps INFO @ Wed, 08 Dec 2021 23:08:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.10_model.r WARNING @ Wed, 08 Dec 2021 23:08:57: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:08:57: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Wed, 08 Dec 2021 23:08:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:08:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:08:59: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:09:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:09:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:09:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.10_summits.bed INFO @ Wed, 08 Dec 2021 23:09:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1688 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:09:01: 3000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:09:07: 4000000 INFO @ Wed, 08 Dec 2021 23:09:13: 5000000 INFO @ Wed, 08 Dec 2021 23:09:19: 6000000 INFO @ Wed, 08 Dec 2021 23:09:19: #1 tag size is determined as 73 bps INFO @ Wed, 08 Dec 2021 23:09:19: #1 tag size = 73 INFO @ Wed, 08 Dec 2021 23:09:19: #1 total tags in treatment: 1123287 INFO @ Wed, 08 Dec 2021 23:09:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:09:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:09:19: #1 tags after filtering in treatment: 662424 INFO @ Wed, 08 Dec 2021 23:09:19: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 08 Dec 2021 23:09:19: #1 finished! INFO @ Wed, 08 Dec 2021 23:09:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:09:19: #2 number of paired peaks: 4367 INFO @ Wed, 08 Dec 2021 23:09:19: start model_add_line... INFO @ Wed, 08 Dec 2021 23:09:19: start X-correlation... INFO @ Wed, 08 Dec 2021 23:09:19: end of X-cor INFO @ Wed, 08 Dec 2021 23:09:19: #2 finished! INFO @ Wed, 08 Dec 2021 23:09:19: #2 predicted fragment length is 114 bps INFO @ Wed, 08 Dec 2021 23:09:19: #2 alternative fragment length(s) may be 114 bps INFO @ Wed, 08 Dec 2021 23:09:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.20_model.r WARNING @ Wed, 08 Dec 2021 23:09:19: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:09:19: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Wed, 08 Dec 2021 23:09:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:09:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:09:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:09:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:09:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:09:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:09:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845650/SRX8845650.20_summits.bed INFO @ Wed, 08 Dec 2021 23:09:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (568 records, 4 fields): 3 millis CompletedMACS2peakCalling