Job ID = 14159573 SRX = SRX8845651 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 39634020 spots for SRR12345958/SRR12345958.sra Written 39634020 spots for SRR12345958/SRR12345958.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159952 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:42 39634020 reads; of these: 39634020 (100.00%) were paired; of these: 20129035 (50.79%) aligned concordantly 0 times 16567118 (41.80%) aligned concordantly exactly 1 time 2937867 (7.41%) aligned concordantly >1 times ---- 20129035 pairs aligned concordantly 0 times; of these: 4112470 (20.43%) aligned discordantly 1 time ---- 16016565 pairs aligned 0 times concordantly or discordantly; of these: 32033130 mates make up the pairs; of these: 29317347 (91.52%) aligned 0 times 1215393 (3.79%) aligned exactly 1 time 1500390 (4.68%) aligned >1 times 63.01% overall alignment rate Time searching: 00:26:43 Overall time: 00:26:43 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 24 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] 20534326 / 23357746 = 0.8791 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 23:15:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.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 23:15:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:15:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:15:16: 1000000 INFO @ Wed, 08 Dec 2021 23:15:22: 2000000 INFO @ Wed, 08 Dec 2021 23:15:27: 3000000 INFO @ Wed, 08 Dec 2021 23:15:33: 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 23:15:39: 5000000 INFO @ Wed, 08 Dec 2021 23:15:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.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 23:15:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:15:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:15:45: 6000000 INFO @ Wed, 08 Dec 2021 23:15:45: 1000000 INFO @ Wed, 08 Dec 2021 23:15:50: 2000000 INFO @ Wed, 08 Dec 2021 23:15:51: 7000000 INFO @ Wed, 08 Dec 2021 23:15:55: 3000000 INFO @ Wed, 08 Dec 2021 23:15:57: 8000000 INFO @ Wed, 08 Dec 2021 23:16:00: 4000000 INFO @ Wed, 08 Dec 2021 23:16:02: #1 tag size is determined as 73 bps INFO @ Wed, 08 Dec 2021 23:16:02: #1 tag size = 73 INFO @ Wed, 08 Dec 2021 23:16:02: #1 total tags in treatment: 2216199 INFO @ Wed, 08 Dec 2021 23:16:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:16:02: #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 23:16:02: #1 tags after filtering in treatment: 1522047 INFO @ Wed, 08 Dec 2021 23:16:02: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 08 Dec 2021 23:16:02: #1 finished! INFO @ Wed, 08 Dec 2021 23:16:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:16:03: #2 number of paired peaks: 2620 INFO @ Wed, 08 Dec 2021 23:16:03: start model_add_line... INFO @ Wed, 08 Dec 2021 23:16:03: start X-correlation... INFO @ Wed, 08 Dec 2021 23:16:03: end of X-cor INFO @ Wed, 08 Dec 2021 23:16:03: #2 finished! INFO @ Wed, 08 Dec 2021 23:16:03: #2 predicted fragment length is 114 bps INFO @ Wed, 08 Dec 2021 23:16:03: #2 alternative fragment length(s) may be 114 bps INFO @ Wed, 08 Dec 2021 23:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.05_model.r WARNING @ Wed, 08 Dec 2021 23:16:03: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:16:03: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Wed, 08 Dec 2021 23:16:03: #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 23:16:03: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:16:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:16:05: 5000000 INFO @ Wed, 08 Dec 2021 23:16:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.05_summits.bed INFO @ Wed, 08 Dec 2021 23:16:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3188 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 23:16:10: 6000000 INFO @ Wed, 08 Dec 2021 23:16:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.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 23:16:11: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:16:11: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:16:15: 7000000 INFO @ Wed, 08 Dec 2021 23:16:17: 1000000 INFO @ Wed, 08 Dec 2021 23:16:20: 8000000 INFO @ Wed, 08 Dec 2021 23:16:23: 2000000 INFO @ Wed, 08 Dec 2021 23:16:24: #1 tag size is determined as 73 bps INFO @ Wed, 08 Dec 2021 23:16:24: #1 tag size = 73 INFO @ Wed, 08 Dec 2021 23:16:24: #1 total tags in treatment: 2216199 INFO @ Wed, 08 Dec 2021 23:16:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:16:24: #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 23:16:24: #1 tags after filtering in treatment: 1522047 INFO @ Wed, 08 Dec 2021 23:16:24: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 08 Dec 2021 23:16:24: #1 finished! INFO @ Wed, 08 Dec 2021 23:16:24: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:16:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:16:25: #2 number of paired peaks: 2620 INFO @ Wed, 08 Dec 2021 23:16:25: start model_add_line... INFO @ Wed, 08 Dec 2021 23:16:25: start X-correlation... INFO @ Wed, 08 Dec 2021 23:16:25: end of X-cor INFO @ Wed, 08 Dec 2021 23:16:25: #2 finished! INFO @ Wed, 08 Dec 2021 23:16:25: #2 predicted fragment length is 114 bps INFO @ Wed, 08 Dec 2021 23:16:25: #2 alternative fragment length(s) may be 114 bps INFO @ Wed, 08 Dec 2021 23:16:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.10_model.r WARNING @ Wed, 08 Dec 2021 23:16:25: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:16:25: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Wed, 08 Dec 2021 23:16:25: #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 23:16:25: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:16:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:16:29: 3000000 INFO @ Wed, 08 Dec 2021 23:16:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:16:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:16:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.10_summits.bed INFO @ Wed, 08 Dec 2021 23:16:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1717 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:16:35: 4000000 INFO @ Wed, 08 Dec 2021 23:16:41: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:16:47: 6000000 INFO @ Wed, 08 Dec 2021 23:16:52: 7000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:16:58: 8000000 INFO @ Wed, 08 Dec 2021 23:17:04: #1 tag size is determined as 73 bps INFO @ Wed, 08 Dec 2021 23:17:04: #1 tag size = 73 INFO @ Wed, 08 Dec 2021 23:17:04: #1 total tags in treatment: 2216199 INFO @ Wed, 08 Dec 2021 23:17:04: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:17:04: #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 23:17:04: #1 tags after filtering in treatment: 1522047 INFO @ Wed, 08 Dec 2021 23:17:04: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 08 Dec 2021 23:17:04: #1 finished! INFO @ Wed, 08 Dec 2021 23:17:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:17:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:17:04: #2 number of paired peaks: 2620 INFO @ Wed, 08 Dec 2021 23:17:04: start model_add_line... INFO @ Wed, 08 Dec 2021 23:17:04: start X-correlation... INFO @ Wed, 08 Dec 2021 23:17:04: end of X-cor INFO @ Wed, 08 Dec 2021 23:17:04: #2 finished! INFO @ Wed, 08 Dec 2021 23:17:04: #2 predicted fragment length is 114 bps INFO @ Wed, 08 Dec 2021 23:17:04: #2 alternative fragment length(s) may be 114 bps INFO @ Wed, 08 Dec 2021 23:17:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.20_model.r WARNING @ Wed, 08 Dec 2021 23:17:04: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:17:04: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Wed, 08 Dec 2021 23:17:04: #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 23:17:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:17:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:17:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:17:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:17:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:17:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845651/SRX8845651.20_summits.bed INFO @ Wed, 08 Dec 2021 23:17:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (621 records, 4 fields): 2 millis CompletedMACS2peakCalling