Job ID = 14159514 SRX = SRX8845628 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6488747 spots for SRR12345973/SRR12345973.sra Written 6488747 spots for SRR12345973/SRR12345973.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159686 ("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: 00:05:54 6488747 reads; of these: 6488747 (100.00%) were paired; of these: 2151871 (33.16%) aligned concordantly 0 times 3810420 (58.72%) aligned concordantly exactly 1 time 526456 (8.11%) aligned concordantly >1 times ---- 2151871 pairs aligned concordantly 0 times; of these: 657889 (30.57%) aligned discordantly 1 time ---- 1493982 pairs aligned 0 times concordantly or discordantly; of these: 2987964 mates make up the pairs; of these: 2634643 (88.18%) aligned 0 times 197359 (6.61%) aligned exactly 1 time 155962 (5.22%) aligned >1 times 79.70% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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] 452641 / 4957230 = 0.0913 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 22:26:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.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 22:26:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:26:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:26:46: 1000000 INFO @ Wed, 08 Dec 2021 22:26:52: 2000000 INFO @ Wed, 08 Dec 2021 22:26:58: 3000000 INFO @ Wed, 08 Dec 2021 22:27:04: 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 22:27:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.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 22:27:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:27:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:27:11: 5000000 INFO @ Wed, 08 Dec 2021 22:27:15: 1000000 INFO @ Wed, 08 Dec 2021 22:27:17: 6000000 INFO @ Wed, 08 Dec 2021 22:27:21: 2000000 INFO @ Wed, 08 Dec 2021 22:27:24: 7000000 INFO @ Wed, 08 Dec 2021 22:27:26: 3000000 INFO @ Wed, 08 Dec 2021 22:27:30: 8000000 INFO @ Wed, 08 Dec 2021 22:27:32: 4000000 INFO @ Wed, 08 Dec 2021 22:27:37: 9000000 INFO @ Wed, 08 Dec 2021 22:27:37: 5000000 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 22:27:39: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:27:39: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:27:39: #1 total tags in treatment: 3945238 INFO @ Wed, 08 Dec 2021 22:27:39: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:27:39: #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 22:27:40: #1 tags after filtering in treatment: 3211014 INFO @ Wed, 08 Dec 2021 22:27:40: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 22:27:40: #1 finished! INFO @ Wed, 08 Dec 2021 22:27:40: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:27:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:27:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.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 22:27:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:27:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:27:40: #2 number of paired peaks: 1906 INFO @ Wed, 08 Dec 2021 22:27:40: start model_add_line... INFO @ Wed, 08 Dec 2021 22:27:40: start X-correlation... INFO @ Wed, 08 Dec 2021 22:27:40: end of X-cor INFO @ Wed, 08 Dec 2021 22:27:40: #2 finished! INFO @ Wed, 08 Dec 2021 22:27:40: #2 predicted fragment length is 112 bps INFO @ Wed, 08 Dec 2021 22:27:40: #2 alternative fragment length(s) may be 112 bps INFO @ Wed, 08 Dec 2021 22:27:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.05_model.r WARNING @ Wed, 08 Dec 2021 22:27:40: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:27:40: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Wed, 08 Dec 2021 22:27:40: #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 22:27:40: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:27:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:27:43: 6000000 INFO @ Wed, 08 Dec 2021 22:27:46: 1000000 INFO @ Wed, 08 Dec 2021 22:27:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:27:48: 7000000 INFO @ Wed, 08 Dec 2021 22:27:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:27:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:27:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.05_summits.bed INFO @ Wed, 08 Dec 2021 22:27:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5630 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:27:53: 2000000 INFO @ Wed, 08 Dec 2021 22:27:54: 8000000 INFO @ Wed, 08 Dec 2021 22:27:59: 9000000 INFO @ Wed, 08 Dec 2021 22:28:00: 3000000 INFO @ Wed, 08 Dec 2021 22:28:02: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:28:02: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:28:02: #1 total tags in treatment: 3945238 INFO @ Wed, 08 Dec 2021 22:28:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:28:02: #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 22:28:02: #1 tags after filtering in treatment: 3211014 INFO @ Wed, 08 Dec 2021 22:28:02: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 22:28:02: #1 finished! INFO @ Wed, 08 Dec 2021 22:28:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:28:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:28:02: #2 number of paired peaks: 1906 INFO @ Wed, 08 Dec 2021 22:28:02: start model_add_line... INFO @ Wed, 08 Dec 2021 22:28:02: start X-correlation... INFO @ Wed, 08 Dec 2021 22:28:02: end of X-cor INFO @ Wed, 08 Dec 2021 22:28:02: #2 finished! INFO @ Wed, 08 Dec 2021 22:28:02: #2 predicted fragment length is 112 bps INFO @ Wed, 08 Dec 2021 22:28:02: #2 alternative fragment length(s) may be 112 bps INFO @ Wed, 08 Dec 2021 22:28:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.10_model.r WARNING @ Wed, 08 Dec 2021 22:28:02: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:28:02: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Wed, 08 Dec 2021 22:28:02: #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 22:28:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:28:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:28:06: 4000000 INFO @ Wed, 08 Dec 2021 22:28:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:28:12: 5000000 INFO @ Wed, 08 Dec 2021 22:28:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:28:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:28:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.10_summits.bed INFO @ Wed, 08 Dec 2021 22:28:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3423 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:28:19: 6000000 INFO @ Wed, 08 Dec 2021 22:28:25: 7000000 INFO @ Wed, 08 Dec 2021 22:28:31: 8000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:28:37: 9000000 INFO @ Wed, 08 Dec 2021 22:28:40: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:28:40: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:28:40: #1 total tags in treatment: 3945238 INFO @ Wed, 08 Dec 2021 22:28:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:28:40: #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 22:28:40: #1 tags after filtering in treatment: 3211014 INFO @ Wed, 08 Dec 2021 22:28:40: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 22:28:40: #1 finished! INFO @ Wed, 08 Dec 2021 22:28:40: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:28:40: #2 number of paired peaks: 1906 INFO @ Wed, 08 Dec 2021 22:28:40: start model_add_line... INFO @ Wed, 08 Dec 2021 22:28:40: start X-correlation... INFO @ Wed, 08 Dec 2021 22:28:40: end of X-cor INFO @ Wed, 08 Dec 2021 22:28:40: #2 finished! INFO @ Wed, 08 Dec 2021 22:28:40: #2 predicted fragment length is 112 bps INFO @ Wed, 08 Dec 2021 22:28:40: #2 alternative fragment length(s) may be 112 bps INFO @ Wed, 08 Dec 2021 22:28:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.20_model.r WARNING @ Wed, 08 Dec 2021 22:28:40: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:28:40: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Wed, 08 Dec 2021 22:28:40: #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 22:28:40: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:28:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:28:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:28:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:28:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:28:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845628/SRX8845628.20_summits.bed INFO @ Wed, 08 Dec 2021 22:28:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1635 records, 4 fields): 3 millis CompletedMACS2peakCalling