Job ID = 12264751 SRX = SRX2333004 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 31364016 spots for SRR5000684/SRR5000684.sra Written 31364016 spots for SRR5000684/SRR5000684.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265836 ("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: 02:22:24 31364016 reads; of these: 31364016 (100.00%) were paired; of these: 15225166 (48.54%) aligned concordantly 0 times 3361737 (10.72%) aligned concordantly exactly 1 time 12777113 (40.74%) aligned concordantly >1 times ---- 15225166 pairs aligned concordantly 0 times; of these: 1212153 (7.96%) aligned discordantly 1 time ---- 14013013 pairs aligned 0 times concordantly or discordantly; of these: 28026026 mates make up the pairs; of these: 23844830 (85.08%) aligned 0 times 836226 (2.98%) aligned exactly 1 time 3344970 (11.94%) aligned >1 times 61.99% overall alignment rate Time searching: 02:22:24 Overall time: 02:22:24 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] 8586746 / 17199130 = 0.4993 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:36:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.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 @ Sat, 03 Apr 2021 08:36:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:36:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:37:01: 1000000 INFO @ Sat, 03 Apr 2021 08:37:09: 2000000 INFO @ Sat, 03 Apr 2021 08:37:18: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:37:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.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 @ Sat, 03 Apr 2021 08:37:22: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:37:22: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:37:27: 4000000 INFO @ Sat, 03 Apr 2021 08:37:32: 1000000 INFO @ Sat, 03 Apr 2021 08:37:36: 5000000 INFO @ Sat, 03 Apr 2021 08:37:42: 2000000 INFO @ Sat, 03 Apr 2021 08:37:47: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:37:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.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 @ Sat, 03 Apr 2021 08:37:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:37:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:37:52: 3000000 INFO @ Sat, 03 Apr 2021 08:37:57: 7000000 INFO @ Sat, 03 Apr 2021 08:38:03: 4000000 INFO @ Sat, 03 Apr 2021 08:38:03: 1000000 INFO @ Sat, 03 Apr 2021 08:38:08: 8000000 INFO @ Sat, 03 Apr 2021 08:38:14: 5000000 INFO @ Sat, 03 Apr 2021 08:38:14: 2000000 INFO @ Sat, 03 Apr 2021 08:38:20: 9000000 INFO @ Sat, 03 Apr 2021 08:38:25: 6000000 INFO @ Sat, 03 Apr 2021 08:38:26: 3000000 INFO @ Sat, 03 Apr 2021 08:38:30: 10000000 INFO @ Sat, 03 Apr 2021 08:38:36: 7000000 INFO @ Sat, 03 Apr 2021 08:38:37: 4000000 INFO @ Sat, 03 Apr 2021 08:38:42: 11000000 INFO @ Sat, 03 Apr 2021 08:38:47: 8000000 INFO @ Sat, 03 Apr 2021 08:38:48: 5000000 INFO @ Sat, 03 Apr 2021 08:38:53: 12000000 INFO @ Sat, 03 Apr 2021 08:38:58: 9000000 INFO @ Sat, 03 Apr 2021 08:38:59: 6000000 INFO @ Sat, 03 Apr 2021 08:39:04: 13000000 INFO @ Sat, 03 Apr 2021 08:39:09: 10000000 INFO @ Sat, 03 Apr 2021 08:39:10: 7000000 INFO @ Sat, 03 Apr 2021 08:39:15: 14000000 INFO @ Sat, 03 Apr 2021 08:39:20: 11000000 INFO @ Sat, 03 Apr 2021 08:39:21: 8000000 INFO @ Sat, 03 Apr 2021 08:39:26: 15000000 INFO @ Sat, 03 Apr 2021 08:39:30: 12000000 INFO @ Sat, 03 Apr 2021 08:39:32: 9000000 INFO @ Sat, 03 Apr 2021 08:39:37: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:39:42: 13000000 INFO @ Sat, 03 Apr 2021 08:39:43: 10000000 INFO @ Sat, 03 Apr 2021 08:39:48: 17000000 INFO @ Sat, 03 Apr 2021 08:39:52: 14000000 INFO @ Sat, 03 Apr 2021 08:39:54: 11000000 INFO @ Sat, 03 Apr 2021 08:39:58: 18000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:40:03: 15000000 INFO @ Sat, 03 Apr 2021 08:40:05: 12000000 INFO @ Sat, 03 Apr 2021 08:40:10: 19000000 INFO @ Sat, 03 Apr 2021 08:40:15: 16000000 INFO @ Sat, 03 Apr 2021 08:40:17: 13000000 INFO @ Sat, 03 Apr 2021 08:40:21: 20000000 INFO @ Sat, 03 Apr 2021 08:40:26: 17000000 INFO @ Sat, 03 Apr 2021 08:40:28: 14000000 INFO @ Sat, 03 Apr 2021 08:40:32: 21000000 INFO @ Sat, 03 Apr 2021 08:40:37: 18000000 INFO @ Sat, 03 Apr 2021 08:40:39: 15000000 INFO @ Sat, 03 Apr 2021 08:40:40: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 08:40:40: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 08:40:40: #1 total tags in treatment: 7900486 INFO @ Sat, 03 Apr 2021 08:40:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:40:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:40:40: #1 tags after filtering in treatment: 3315433 INFO @ Sat, 03 Apr 2021 08:40:40: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 03 Apr 2021 08:40:40: #1 finished! INFO @ Sat, 03 Apr 2021 08:40:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:40:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:40:41: #2 number of paired peaks: 5790 INFO @ Sat, 03 Apr 2021 08:40:41: start model_add_line... INFO @ Sat, 03 Apr 2021 08:40:41: start X-correlation... INFO @ Sat, 03 Apr 2021 08:40:41: end of X-cor INFO @ Sat, 03 Apr 2021 08:40:41: #2 finished! INFO @ Sat, 03 Apr 2021 08:40:41: #2 predicted fragment length is 142 bps INFO @ Sat, 03 Apr 2021 08:40:41: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 03 Apr 2021 08:40:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.05_model.r WARNING @ Sat, 03 Apr 2021 08:40:41: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:40:41: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Sat, 03 Apr 2021 08:40:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:40:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:40:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:40:47: 19000000 INFO @ Sat, 03 Apr 2021 08:40:50: 16000000 INFO @ Sat, 03 Apr 2021 08:40:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.05_summits.bed INFO @ Sat, 03 Apr 2021 08:40:56: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (7057 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:40:58: 20000000 INFO @ Sat, 03 Apr 2021 08:41:00: 17000000 INFO @ Sat, 03 Apr 2021 08:41:09: 21000000 INFO @ Sat, 03 Apr 2021 08:41:10: 18000000 INFO @ Sat, 03 Apr 2021 08:41:16: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 08:41:16: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 08:41:16: #1 total tags in treatment: 7900486 INFO @ Sat, 03 Apr 2021 08:41:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:41:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:41:16: #1 tags after filtering in treatment: 3315433 INFO @ Sat, 03 Apr 2021 08:41:16: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 03 Apr 2021 08:41:16: #1 finished! INFO @ Sat, 03 Apr 2021 08:41:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:41:17: #2 number of paired peaks: 5790 INFO @ Sat, 03 Apr 2021 08:41:17: start model_add_line... INFO @ Sat, 03 Apr 2021 08:41:17: start X-correlation... INFO @ Sat, 03 Apr 2021 08:41:17: end of X-cor INFO @ Sat, 03 Apr 2021 08:41:17: #2 finished! INFO @ Sat, 03 Apr 2021 08:41:17: #2 predicted fragment length is 142 bps INFO @ Sat, 03 Apr 2021 08:41:17: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 03 Apr 2021 08:41:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.10_model.r WARNING @ Sat, 03 Apr 2021 08:41:17: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:41:17: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Sat, 03 Apr 2021 08:41:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:41:17: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:41:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:41:20: 19000000 INFO @ Sat, 03 Apr 2021 08:41:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:41:29: 20000000 INFO @ Sat, 03 Apr 2021 08:41:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:41:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:41:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.10_summits.bed INFO @ Sat, 03 Apr 2021 08:41:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4963 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:41:39: 21000000 INFO @ Sat, 03 Apr 2021 08:41:46: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 08:41:46: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 08:41:46: #1 total tags in treatment: 7900486 INFO @ Sat, 03 Apr 2021 08:41:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:41:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:41:46: #1 tags after filtering in treatment: 3315433 INFO @ Sat, 03 Apr 2021 08:41:46: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 03 Apr 2021 08:41:46: #1 finished! INFO @ Sat, 03 Apr 2021 08:41:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:41:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:41:47: #2 number of paired peaks: 5790 INFO @ Sat, 03 Apr 2021 08:41:47: start model_add_line... INFO @ Sat, 03 Apr 2021 08:41:47: start X-correlation... INFO @ Sat, 03 Apr 2021 08:41:47: end of X-cor INFO @ Sat, 03 Apr 2021 08:41:47: #2 finished! INFO @ Sat, 03 Apr 2021 08:41:47: #2 predicted fragment length is 142 bps INFO @ Sat, 03 Apr 2021 08:41:47: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 03 Apr 2021 08:41:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.20_model.r WARNING @ Sat, 03 Apr 2021 08:41:47: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:41:47: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Sat, 03 Apr 2021 08:41:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:41:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:41:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:41:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:42:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:42:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:42:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2333004/SRX2333004.20_summits.bed INFO @ Sat, 03 Apr 2021 08:42:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2467 records, 4 fields): 4 millis CompletedMACS2peakCalling