Job ID = 14158412 SRX = SRX10641195 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-08T08:30:35 prefetch.2.10.7: 1) Downloading 'SRR14280083'... 2021-12-08T08:30:35 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T08:47:29 prefetch.2.10.7: HTTPS download succeed 2021-12-08T08:47:29 prefetch.2.10.7: 1) 'SRR14280083' was downloaded successfully 2021-12-08T08:47:29 prefetch.2.10.7: 'SRR14280083' has 0 unresolved dependencies Read 20466222 spots for SRR14280083/SRR14280083.sra Written 20466222 spots for SRR14280083/SRR14280083.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159242 ("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: 00:32:45 20466222 reads; of these: 20466222 (100.00%) were paired; of these: 14382321 (70.27%) aligned concordantly 0 times 2892733 (14.13%) aligned concordantly exactly 1 time 3191168 (15.59%) aligned concordantly >1 times ---- 14382321 pairs aligned concordantly 0 times; of these: 1447261 (10.06%) aligned discordantly 1 time ---- 12935060 pairs aligned 0 times concordantly or discordantly; of these: 25870120 mates make up the pairs; of these: 24963245 (96.49%) aligned 0 times 416850 (1.61%) aligned exactly 1 time 490025 (1.89%) aligned >1 times 39.01% overall alignment rate Time searching: 00:32:45 Overall time: 00:32:45 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 12 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] 1928549 / 7498109 = 0.2572 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 18:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.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 18:30:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:30:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:30:40: 1000000 INFO @ Wed, 08 Dec 2021 18:30:48: 2000000 INFO @ Wed, 08 Dec 2021 18:30:56: 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 18:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.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 18:31:02: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:31:02: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:31:03: 4000000 INFO @ Wed, 08 Dec 2021 18:31:09: 1000000 INFO @ Wed, 08 Dec 2021 18:31:11: 5000000 INFO @ Wed, 08 Dec 2021 18:31:15: 2000000 INFO @ Wed, 08 Dec 2021 18:31:18: 6000000 INFO @ Wed, 08 Dec 2021 18:31:21: 3000000 INFO @ Wed, 08 Dec 2021 18:31:26: 7000000 INFO @ Wed, 08 Dec 2021 18:31:28: 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 18:31:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.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 18:31:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:31:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:31:34: 8000000 INFO @ Wed, 08 Dec 2021 18:31:34: 5000000 INFO @ Wed, 08 Dec 2021 18:31:40: 1000000 INFO @ Wed, 08 Dec 2021 18:31:41: 6000000 INFO @ Wed, 08 Dec 2021 18:31:42: 9000000 INFO @ Wed, 08 Dec 2021 18:31:47: 7000000 INFO @ Wed, 08 Dec 2021 18:31:47: 2000000 INFO @ Wed, 08 Dec 2021 18:31:49: 10000000 INFO @ Wed, 08 Dec 2021 18:31:53: 8000000 INFO @ Wed, 08 Dec 2021 18:31:55: 3000000 INFO @ Wed, 08 Dec 2021 18:31:57: 11000000 INFO @ Wed, 08 Dec 2021 18:32:00: 9000000 INFO @ Wed, 08 Dec 2021 18:32:02: 4000000 INFO @ Wed, 08 Dec 2021 18:32:04: 12000000 INFO @ Wed, 08 Dec 2021 18:32:05: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:32:05: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:32:05: #1 total tags in treatment: 4309877 INFO @ Wed, 08 Dec 2021 18:32:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:32:05: #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 18:32:05: #1 tags after filtering in treatment: 2867565 INFO @ Wed, 08 Dec 2021 18:32:05: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 08 Dec 2021 18:32:05: #1 finished! INFO @ Wed, 08 Dec 2021 18:32:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:32:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:32:06: #2 number of paired peaks: 1059 INFO @ Wed, 08 Dec 2021 18:32:06: start model_add_line... INFO @ Wed, 08 Dec 2021 18:32:06: start X-correlation... INFO @ Wed, 08 Dec 2021 18:32:06: end of X-cor INFO @ Wed, 08 Dec 2021 18:32:06: #2 finished! INFO @ Wed, 08 Dec 2021 18:32:06: #2 predicted fragment length is 292 bps INFO @ Wed, 08 Dec 2021 18:32:06: #2 alternative fragment length(s) may be 292 bps INFO @ Wed, 08 Dec 2021 18:32:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.05_model.r WARNING @ Wed, 08 Dec 2021 18:32:06: #2 Since the d (292) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:32:06: #2 You may need to consider one of the other alternative d(s): 292 WARNING @ Wed, 08 Dec 2021 18:32:06: #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 18:32:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:32:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:32:06: 10000000 INFO @ Wed, 08 Dec 2021 18:32:09: 5000000 INFO @ Wed, 08 Dec 2021 18:32:12: 11000000 INFO @ Wed, 08 Dec 2021 18:32:14: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:32:17: 6000000 INFO @ Wed, 08 Dec 2021 18:32:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:32:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:32:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.05_summits.bed INFO @ Wed, 08 Dec 2021 18:32:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1077 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:32:18: 12000000 INFO @ Wed, 08 Dec 2021 18:32:19: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:32:19: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:32:19: #1 total tags in treatment: 4309877 INFO @ Wed, 08 Dec 2021 18:32:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:32:19: #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 18:32:19: #1 tags after filtering in treatment: 2867565 INFO @ Wed, 08 Dec 2021 18:32:19: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 08 Dec 2021 18:32:19: #1 finished! INFO @ Wed, 08 Dec 2021 18:32:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:32:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:32:19: #2 number of paired peaks: 1059 INFO @ Wed, 08 Dec 2021 18:32:19: start model_add_line... INFO @ Wed, 08 Dec 2021 18:32:19: start X-correlation... INFO @ Wed, 08 Dec 2021 18:32:19: end of X-cor INFO @ Wed, 08 Dec 2021 18:32:19: #2 finished! INFO @ Wed, 08 Dec 2021 18:32:19: #2 predicted fragment length is 292 bps INFO @ Wed, 08 Dec 2021 18:32:19: #2 alternative fragment length(s) may be 292 bps INFO @ Wed, 08 Dec 2021 18:32:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.10_model.r WARNING @ Wed, 08 Dec 2021 18:32:19: #2 Since the d (292) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:32:19: #2 You may need to consider one of the other alternative d(s): 292 WARNING @ Wed, 08 Dec 2021 18:32:19: #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 18:32:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:32:24: 7000000 INFO @ Wed, 08 Dec 2021 18:32:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:32:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:32:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:32:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.10_summits.bed INFO @ Wed, 08 Dec 2021 18:32:31: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (665 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:32:32: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:32:39: 9000000 INFO @ Wed, 08 Dec 2021 18:32:46: 10000000 INFO @ Wed, 08 Dec 2021 18:32:53: 11000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:33:00: 12000000 INFO @ Wed, 08 Dec 2021 18:33:01: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:33:01: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:33:01: #1 total tags in treatment: 4309877 INFO @ Wed, 08 Dec 2021 18:33:01: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:33:01: #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 18:33:01: #1 tags after filtering in treatment: 2867565 INFO @ Wed, 08 Dec 2021 18:33:01: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 08 Dec 2021 18:33:01: #1 finished! INFO @ Wed, 08 Dec 2021 18:33:01: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:33:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:33:02: #2 number of paired peaks: 1059 INFO @ Wed, 08 Dec 2021 18:33:02: start model_add_line... INFO @ Wed, 08 Dec 2021 18:33:02: start X-correlation... INFO @ Wed, 08 Dec 2021 18:33:02: end of X-cor INFO @ Wed, 08 Dec 2021 18:33:02: #2 finished! INFO @ Wed, 08 Dec 2021 18:33:02: #2 predicted fragment length is 292 bps INFO @ Wed, 08 Dec 2021 18:33:02: #2 alternative fragment length(s) may be 292 bps INFO @ Wed, 08 Dec 2021 18:33:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.20_model.r WARNING @ Wed, 08 Dec 2021 18:33:02: #2 Since the d (292) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:33:02: #2 You may need to consider one of the other alternative d(s): 292 WARNING @ Wed, 08 Dec 2021 18:33:02: #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 18:33:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:33:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:33:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:33:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641195/SRX10641195.20_summits.bed INFO @ Wed, 08 Dec 2021 18:33:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (442 records, 4 fields): 8 millis CompletedMACS2peakCalling