Job ID = 14159579 SRX = SRX8845656 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6984741 spots for SRR12345963/SRR12345963.sra Written 6984741 spots for SRR12345963/SRR12345963.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159935 ("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: 00:09:34 6984741 reads; of these: 6984741 (100.00%) were paired; of these: 2245584 (32.15%) aligned concordantly 0 times 3935149 (56.34%) aligned concordantly exactly 1 time 804008 (11.51%) aligned concordantly >1 times ---- 2245584 pairs aligned concordantly 0 times; of these: 735266 (32.74%) aligned discordantly 1 time ---- 1510318 pairs aligned 0 times concordantly or discordantly; of these: 3020636 mates make up the pairs; of these: 2525444 (83.61%) aligned 0 times 208251 (6.89%) aligned exactly 1 time 286941 (9.50%) aligned >1 times 81.92% overall alignment rate Time searching: 00:09:34 Overall time: 00:09:34 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 8 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] 860967 / 5419824 = 0.1589 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 23:00:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.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 23:00:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:00:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:00:10: 1000000 INFO @ Wed, 08 Dec 2021 23:00:17: 2000000 INFO @ Wed, 08 Dec 2021 23:00:25: 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 @ Wed, 08 Dec 2021 23:00:32: 4000000 INFO @ Wed, 08 Dec 2021 23:00:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.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 23:00:33: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:00:33: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:00:39: 5000000 INFO @ Wed, 08 Dec 2021 23:00:45: 1000000 INFO @ Wed, 08 Dec 2021 23:00:47: 6000000 INFO @ Wed, 08 Dec 2021 23:00:54: 7000000 INFO @ Wed, 08 Dec 2021 23:00:57: 2000000 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 23:01:02: 8000000 INFO @ Wed, 08 Dec 2021 23:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.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 23:01:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:01:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:01:07: 3000000 INFO @ Wed, 08 Dec 2021 23:01:11: 9000000 INFO @ Wed, 08 Dec 2021 23:01:14: 1000000 INFO @ Wed, 08 Dec 2021 23:01:16: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 23:01:16: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 23:01:16: #1 total tags in treatment: 3991862 INFO @ Wed, 08 Dec 2021 23:01:16: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:01:16: #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 23:01:17: #1 tags after filtering in treatment: 2939905 INFO @ Wed, 08 Dec 2021 23:01:17: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 08 Dec 2021 23:01:17: #1 finished! INFO @ Wed, 08 Dec 2021 23:01:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:01:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:01:17: #2 number of paired peaks: 2950 INFO @ Wed, 08 Dec 2021 23:01:17: start model_add_line... INFO @ Wed, 08 Dec 2021 23:01:17: start X-correlation... INFO @ Wed, 08 Dec 2021 23:01:17: end of X-cor INFO @ Wed, 08 Dec 2021 23:01:17: #2 finished! INFO @ Wed, 08 Dec 2021 23:01:17: #2 predicted fragment length is 116 bps INFO @ Wed, 08 Dec 2021 23:01:17: #2 alternative fragment length(s) may be 116 bps INFO @ Wed, 08 Dec 2021 23:01:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.05_model.r WARNING @ Wed, 08 Dec 2021 23:01:17: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:01:17: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Wed, 08 Dec 2021 23:01:17: #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 23:01:17: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:01:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:01:20: 4000000 INFO @ Wed, 08 Dec 2021 23:01:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:01:25: 2000000 INFO @ Wed, 08 Dec 2021 23:01:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:01:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:01:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.05_summits.bed INFO @ Wed, 08 Dec 2021 23:01:28: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6408 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:01:33: 5000000 INFO @ Wed, 08 Dec 2021 23:01:36: 3000000 INFO @ Wed, 08 Dec 2021 23:01:46: 6000000 INFO @ Wed, 08 Dec 2021 23:01:48: 4000000 INFO @ Wed, 08 Dec 2021 23:01:57: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:01:58: 5000000 INFO @ Wed, 08 Dec 2021 23:02:09: 6000000 INFO @ Wed, 08 Dec 2021 23:02:10: 8000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:02:19: 7000000 INFO @ Wed, 08 Dec 2021 23:02:22: 9000000 INFO @ Wed, 08 Dec 2021 23:02:30: 8000000 INFO @ Wed, 08 Dec 2021 23:02:30: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 23:02:30: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 23:02:30: #1 total tags in treatment: 3991862 INFO @ Wed, 08 Dec 2021 23:02:30: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:02:30: #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 23:02:30: #1 tags after filtering in treatment: 2939905 INFO @ Wed, 08 Dec 2021 23:02:30: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 08 Dec 2021 23:02:30: #1 finished! INFO @ Wed, 08 Dec 2021 23:02:30: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:02:31: #2 number of paired peaks: 2950 INFO @ Wed, 08 Dec 2021 23:02:31: start model_add_line... INFO @ Wed, 08 Dec 2021 23:02:31: start X-correlation... INFO @ Wed, 08 Dec 2021 23:02:31: end of X-cor INFO @ Wed, 08 Dec 2021 23:02:31: #2 finished! INFO @ Wed, 08 Dec 2021 23:02:31: #2 predicted fragment length is 116 bps INFO @ Wed, 08 Dec 2021 23:02:31: #2 alternative fragment length(s) may be 116 bps INFO @ Wed, 08 Dec 2021 23:02:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.10_model.r WARNING @ Wed, 08 Dec 2021 23:02:31: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:02:31: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Wed, 08 Dec 2021 23:02:31: #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 23:02:31: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:02:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:02:41: 9000000 INFO @ Wed, 08 Dec 2021 23:02:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:02:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:02:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.10_summits.bed INFO @ Wed, 08 Dec 2021 23:02:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4075 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:02:48: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 23:02:48: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 23:02:48: #1 total tags in treatment: 3991862 INFO @ Wed, 08 Dec 2021 23:02:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:02:48: #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 23:02:49: #1 tags after filtering in treatment: 2939905 INFO @ Wed, 08 Dec 2021 23:02:49: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 08 Dec 2021 23:02:49: #1 finished! INFO @ Wed, 08 Dec 2021 23:02:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:02:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:02:49: #2 number of paired peaks: 2950 INFO @ Wed, 08 Dec 2021 23:02:49: start model_add_line... INFO @ Wed, 08 Dec 2021 23:02:49: start X-correlation... INFO @ Wed, 08 Dec 2021 23:02:49: end of X-cor INFO @ Wed, 08 Dec 2021 23:02:49: #2 finished! INFO @ Wed, 08 Dec 2021 23:02:49: #2 predicted fragment length is 116 bps INFO @ Wed, 08 Dec 2021 23:02:49: #2 alternative fragment length(s) may be 116 bps INFO @ Wed, 08 Dec 2021 23:02:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.20_model.r WARNING @ Wed, 08 Dec 2021 23:02:49: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:02:49: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Wed, 08 Dec 2021 23:02:49: #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 23:02:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:02:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:02:56: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:03:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845656/SRX8845656.20_summits.bed INFO @ Wed, 08 Dec 2021 23:03:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2244 records, 4 fields): 4 millis CompletedMACS2peakCalling