Job ID = 14158385 SRX = SRX10641180 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18376068 spots for SRR14280098/SRR14280098.sra Written 18376068 spots for SRR14280098/SRR14280098.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159004 ("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: 00:31:41 18376068 reads; of these: 18376068 (100.00%) were paired; of these: 11311938 (61.56%) aligned concordantly 0 times 6301993 (34.29%) aligned concordantly exactly 1 time 762137 (4.15%) aligned concordantly >1 times ---- 11311938 pairs aligned concordantly 0 times; of these: 2944959 (26.03%) aligned discordantly 1 time ---- 8366979 pairs aligned 0 times concordantly or discordantly; of these: 16733958 mates make up the pairs; of these: 15534506 (92.83%) aligned 0 times 645116 (3.86%) aligned exactly 1 time 554336 (3.31%) aligned >1 times 57.73% overall alignment rate Time searching: 00:31:41 Overall time: 00:31:41 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 16 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] 1193445 / 9987169 = 0.1195 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 17:25:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.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 17:25:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:25:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:25:24: 1000000 INFO @ Wed, 08 Dec 2021 17:25:34: 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 @ Wed, 08 Dec 2021 17:25:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.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 17:25:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:25:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:25:48: 3000000 INFO @ Wed, 08 Dec 2021 17:25:57: 1000000 INFO @ Wed, 08 Dec 2021 17:26:04: 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 @ Wed, 08 Dec 2021 17:26:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.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 17:26:11: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:26:11: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:26:13: 2000000 INFO @ Wed, 08 Dec 2021 17:26:16: 5000000 INFO @ Wed, 08 Dec 2021 17:26:25: 1000000 INFO @ Wed, 08 Dec 2021 17:26:29: 6000000 INFO @ Wed, 08 Dec 2021 17:26:30: 3000000 INFO @ Wed, 08 Dec 2021 17:26:39: 2000000 INFO @ Wed, 08 Dec 2021 17:26:42: 7000000 INFO @ Wed, 08 Dec 2021 17:26:44: 4000000 INFO @ Wed, 08 Dec 2021 17:26:53: 3000000 INFO @ Wed, 08 Dec 2021 17:26:54: 8000000 INFO @ Wed, 08 Dec 2021 17:27:02: 5000000 INFO @ Wed, 08 Dec 2021 17:27:07: 9000000 INFO @ Wed, 08 Dec 2021 17:27:09: 4000000 INFO @ Wed, 08 Dec 2021 17:27:19: 10000000 INFO @ Wed, 08 Dec 2021 17:27:21: 6000000 INFO @ Wed, 08 Dec 2021 17:27:23: 5000000 INFO @ Wed, 08 Dec 2021 17:27:30: 11000000 INFO @ Wed, 08 Dec 2021 17:27:37: 6000000 INFO @ Wed, 08 Dec 2021 17:27:39: 7000000 INFO @ Wed, 08 Dec 2021 17:27:41: 12000000 INFO @ Wed, 08 Dec 2021 17:27:51: 7000000 INFO @ Wed, 08 Dec 2021 17:27:53: 13000000 INFO @ Wed, 08 Dec 2021 17:27:56: 8000000 INFO @ Wed, 08 Dec 2021 17:28:05: 14000000 INFO @ Wed, 08 Dec 2021 17:28:06: 8000000 INFO @ Wed, 08 Dec 2021 17:28:14: 9000000 INFO @ Wed, 08 Dec 2021 17:28:16: 15000000 INFO @ Wed, 08 Dec 2021 17:28:20: 9000000 INFO @ Wed, 08 Dec 2021 17:28:27: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:28:32: 10000000 INFO @ Wed, 08 Dec 2021 17:28:34: 10000000 INFO @ Wed, 08 Dec 2021 17:28:38: 17000000 INFO @ Wed, 08 Dec 2021 17:28:48: 11000000 INFO @ Wed, 08 Dec 2021 17:28:49: 18000000 INFO @ Wed, 08 Dec 2021 17:28:50: 11000000 INFO @ Wed, 08 Dec 2021 17:28:58: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:28:58: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:28:58: #1 total tags in treatment: 6137874 INFO @ Wed, 08 Dec 2021 17:28:58: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:28:58: #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 17:28:58: #1 tags after filtering in treatment: 5714816 INFO @ Wed, 08 Dec 2021 17:28:58: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:28:58: #1 finished! INFO @ Wed, 08 Dec 2021 17:28:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:28:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:28:59: #2 number of paired peaks: 1788 INFO @ Wed, 08 Dec 2021 17:28:59: start model_add_line... INFO @ Wed, 08 Dec 2021 17:28:59: start X-correlation... INFO @ Wed, 08 Dec 2021 17:28:59: end of X-cor INFO @ Wed, 08 Dec 2021 17:28:59: #2 finished! INFO @ Wed, 08 Dec 2021 17:28:59: #2 predicted fragment length is 254 bps INFO @ Wed, 08 Dec 2021 17:28:59: #2 alternative fragment length(s) may be 4,254 bps INFO @ Wed, 08 Dec 2021 17:28:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.05_model.r WARNING @ Wed, 08 Dec 2021 17:28:59: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:28:59: #2 You may need to consider one of the other alternative d(s): 4,254 WARNING @ Wed, 08 Dec 2021 17:28:59: #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 17:28:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:28:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:29:03: 12000000 INFO @ Wed, 08 Dec 2021 17:29:08: 12000000 INFO @ Wed, 08 Dec 2021 17:29:16: 13000000 INFO @ Wed, 08 Dec 2021 17:29:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 17:29:25: 13000000 INFO @ Wed, 08 Dec 2021 17:29:29: 14000000 INFO @ Wed, 08 Dec 2021 17:29:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:29:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:29:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.05_summits.bed INFO @ Wed, 08 Dec 2021 17:29:30: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1968 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:29:42: 15000000 INFO @ Wed, 08 Dec 2021 17:29:43: 14000000 INFO @ Wed, 08 Dec 2021 17:29:55: 16000000 INFO @ Wed, 08 Dec 2021 17:30:01: 15000000 INFO @ Wed, 08 Dec 2021 17:30:08: 17000000 INFO @ Wed, 08 Dec 2021 17:30:18: 16000000 INFO @ Wed, 08 Dec 2021 17:30:21: 18000000 INFO @ Wed, 08 Dec 2021 17:30:32: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:30:32: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:30:32: #1 total tags in treatment: 6137874 INFO @ Wed, 08 Dec 2021 17:30:32: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:30:32: #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 17:30:32: #1 tags after filtering in treatment: 5714816 INFO @ Wed, 08 Dec 2021 17:30:32: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:30:32: #1 finished! INFO @ Wed, 08 Dec 2021 17:30:32: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:30:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:30:33: #2 number of paired peaks: 1788 INFO @ Wed, 08 Dec 2021 17:30:33: start model_add_line... INFO @ Wed, 08 Dec 2021 17:30:33: start X-correlation... INFO @ Wed, 08 Dec 2021 17:30:33: end of X-cor INFO @ Wed, 08 Dec 2021 17:30:33: #2 finished! INFO @ Wed, 08 Dec 2021 17:30:33: #2 predicted fragment length is 254 bps INFO @ Wed, 08 Dec 2021 17:30:33: #2 alternative fragment length(s) may be 4,254 bps INFO @ Wed, 08 Dec 2021 17:30:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.20_model.r WARNING @ Wed, 08 Dec 2021 17:30:33: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:30:33: #2 You may need to consider one of the other alternative d(s): 4,254 WARNING @ Wed, 08 Dec 2021 17:30:33: #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 17:30:33: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:30:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:30:34: 17000000 INFO @ Wed, 08 Dec 2021 17:30:51: 18000000 INFO @ Wed, 08 Dec 2021 17:30:54: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:31:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.20_peaks.xls INFO @ Wed, 08 Dec 2021 17:31:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:31:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.20_summits.bed INFO @ Wed, 08 Dec 2021 17:31:03: Done! INFO @ Wed, 08 Dec 2021 17:31:03: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:31:03: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:31:03: #1 total tags in treatment: 6137874 INFO @ Wed, 08 Dec 2021 17:31:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:31:03: #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 17:31:04: #1 tags after filtering in treatment: 5714816 INFO @ Wed, 08 Dec 2021 17:31:04: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:31:04: #1 finished! INFO @ Wed, 08 Dec 2021 17:31:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:31:04: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (370 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:31:04: #2 number of paired peaks: 1788 INFO @ Wed, 08 Dec 2021 17:31:04: start model_add_line... INFO @ Wed, 08 Dec 2021 17:31:04: start X-correlation... INFO @ Wed, 08 Dec 2021 17:31:04: end of X-cor INFO @ Wed, 08 Dec 2021 17:31:04: #2 finished! INFO @ Wed, 08 Dec 2021 17:31:04: #2 predicted fragment length is 254 bps INFO @ Wed, 08 Dec 2021 17:31:04: #2 alternative fragment length(s) may be 4,254 bps INFO @ Wed, 08 Dec 2021 17:31:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.10_model.r WARNING @ Wed, 08 Dec 2021 17:31:04: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:31:04: #2 You may need to consider one of the other alternative d(s): 4,254 WARNING @ Wed, 08 Dec 2021 17:31:04: #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 17:31:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:31:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:31:26: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:31:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.10_peaks.xls INFO @ Wed, 08 Dec 2021 17:31:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:31:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641180/SRX10641180.10_summits.bed INFO @ Wed, 08 Dec 2021 17:31:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (866 records, 4 fields): 5 millis CompletedMACS2peakCalling