Job ID = 14160417 SRX = SRX9567196 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13969671 spots for SRR13125171/SRR13125171.sra Written 13969671 spots for SRR13125171/SRR13125171.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160607 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:44 13969671 reads; of these: 13969671 (100.00%) were paired; of these: 5443818 (38.97%) aligned concordantly 0 times 7341773 (52.56%) aligned concordantly exactly 1 time 1184080 (8.48%) aligned concordantly >1 times ---- 5443818 pairs aligned concordantly 0 times; of these: 4010080 (73.66%) aligned discordantly 1 time ---- 1433738 pairs aligned 0 times concordantly or discordantly; of these: 2867476 mates make up the pairs; of these: 1109036 (38.68%) aligned 0 times 841065 (29.33%) aligned exactly 1 time 917375 (31.99%) aligned >1 times 96.03% overall alignment rate Time searching: 00:26:45 Overall time: 00:26:45 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] 9587384 / 12530015 = 0.7652 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 02:53:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.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 02:53:47: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:53:47: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:53:55: 1000000 INFO @ Thu, 09 Dec 2021 02:54:03: 2000000 INFO @ Thu, 09 Dec 2021 02:54:11: 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 02:54:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.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 02:54:17: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:54:17: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:54:20: 4000000 INFO @ Thu, 09 Dec 2021 02:54:27: 1000000 INFO @ Thu, 09 Dec 2021 02:54:30: 5000000 INFO @ Thu, 09 Dec 2021 02:54:36: 2000000 INFO @ Thu, 09 Dec 2021 02:54:40: 6000000 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 02:54:46: 3000000 INFO @ Thu, 09 Dec 2021 02:54:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.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 02:54:47: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:54:47: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:54:50: 7000000 INFO @ Thu, 09 Dec 2021 02:54:57: 4000000 INFO @ Thu, 09 Dec 2021 02:54:57: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:54:57: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:54:57: #1 total tags in treatment: 1997808 INFO @ Thu, 09 Dec 2021 02:54:57: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:54:57: #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 02:54:57: #1 tags after filtering in treatment: 1834300 INFO @ Thu, 09 Dec 2021 02:54:57: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 02:54:57: #1 finished! INFO @ Thu, 09 Dec 2021 02:54:57: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:54:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:54:58: #2 number of paired peaks: 1818 INFO @ Thu, 09 Dec 2021 02:54:58: start model_add_line... INFO @ Thu, 09 Dec 2021 02:54:58: start X-correlation... INFO @ Thu, 09 Dec 2021 02:54:58: end of X-cor INFO @ Thu, 09 Dec 2021 02:54:58: #2 finished! INFO @ Thu, 09 Dec 2021 02:54:58: #2 predicted fragment length is 250 bps INFO @ Thu, 09 Dec 2021 02:54:58: #2 alternative fragment length(s) may be 250 bps INFO @ Thu, 09 Dec 2021 02:54:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.05_model.r WARNING @ Thu, 09 Dec 2021 02:54:58: #2 Since the d (250) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:54:58: #2 You may need to consider one of the other alternative d(s): 250 WARNING @ Thu, 09 Dec 2021 02:54:58: #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 02:54:58: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:54:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:54:59: 1000000 INFO @ Thu, 09 Dec 2021 02:55:03: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:55:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:55:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:55:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.05_summits.bed INFO @ Thu, 09 Dec 2021 02:55:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (841 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:55:09: 5000000 INFO @ Thu, 09 Dec 2021 02:55:11: 2000000 INFO @ Thu, 09 Dec 2021 02:55:20: 6000000 INFO @ Thu, 09 Dec 2021 02:55:23: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:55:31: 7000000 INFO @ Thu, 09 Dec 2021 02:55:36: 4000000 INFO @ Thu, 09 Dec 2021 02:55:39: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:55:39: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:55:39: #1 total tags in treatment: 1997808 INFO @ Thu, 09 Dec 2021 02:55:39: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:55:39: #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 02:55:39: #1 tags after filtering in treatment: 1834300 INFO @ Thu, 09 Dec 2021 02:55:39: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 02:55:39: #1 finished! INFO @ Thu, 09 Dec 2021 02:55:39: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:55:39: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:55:39: #2 number of paired peaks: 1818 INFO @ Thu, 09 Dec 2021 02:55:39: start model_add_line... INFO @ Thu, 09 Dec 2021 02:55:39: start X-correlation... INFO @ Thu, 09 Dec 2021 02:55:39: end of X-cor INFO @ Thu, 09 Dec 2021 02:55:39: #2 finished! INFO @ Thu, 09 Dec 2021 02:55:39: #2 predicted fragment length is 250 bps INFO @ Thu, 09 Dec 2021 02:55:39: #2 alternative fragment length(s) may be 250 bps INFO @ Thu, 09 Dec 2021 02:55:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.10_model.r WARNING @ Thu, 09 Dec 2021 02:55:39: #2 Since the d (250) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:55:39: #2 You may need to consider one of the other alternative d(s): 250 WARNING @ Thu, 09 Dec 2021 02:55:39: #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 02:55:39: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:55:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:55:44: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:55:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:55:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:55:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.10_summits.bed INFO @ Thu, 09 Dec 2021 02:55:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (486 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:55:47: 5000000 INFO @ Thu, 09 Dec 2021 02:55:58: 6000000 INFO @ Thu, 09 Dec 2021 02:56:08: 7000000 INFO @ Thu, 09 Dec 2021 02:56:15: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:56:15: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:56:15: #1 total tags in treatment: 1997808 INFO @ Thu, 09 Dec 2021 02:56:15: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:56:15: #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 02:56:15: #1 tags after filtering in treatment: 1834300 INFO @ Thu, 09 Dec 2021 02:56:15: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 02:56:15: #1 finished! INFO @ Thu, 09 Dec 2021 02:56:15: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:56:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:56:15: #2 number of paired peaks: 1818 INFO @ Thu, 09 Dec 2021 02:56:15: start model_add_line... INFO @ Thu, 09 Dec 2021 02:56:15: start X-correlation... INFO @ Thu, 09 Dec 2021 02:56:15: end of X-cor INFO @ Thu, 09 Dec 2021 02:56:15: #2 finished! INFO @ Thu, 09 Dec 2021 02:56:15: #2 predicted fragment length is 250 bps INFO @ Thu, 09 Dec 2021 02:56:15: #2 alternative fragment length(s) may be 250 bps INFO @ Thu, 09 Dec 2021 02:56:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.20_model.r WARNING @ Thu, 09 Dec 2021 02:56:15: #2 Since the d (250) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:56:15: #2 You may need to consider one of the other alternative d(s): 250 WARNING @ Thu, 09 Dec 2021 02:56:15: #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 02:56:15: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:56:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:56:20: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:56:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:56:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:56:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567196/SRX9567196.20_summits.bed INFO @ Thu, 09 Dec 2021 02:56:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 17 millis CompletedMACS2peakCalling