Job ID = 14158387 SRX = SRX10641181 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22272042 spots for SRR14280097/SRR14280097.sra Written 22272042 spots for SRR14280097/SRR14280097.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159052 ("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: 00:30:06 22272042 reads; of these: 22272042 (100.00%) were paired; of these: 14172846 (63.64%) aligned concordantly 0 times 7272584 (32.65%) aligned concordantly exactly 1 time 826612 (3.71%) aligned concordantly >1 times ---- 14172846 pairs aligned concordantly 0 times; of these: 2413995 (17.03%) aligned discordantly 1 time ---- 11758851 pairs aligned 0 times concordantly or discordantly; of these: 23517702 mates make up the pairs; of these: 22543444 (95.86%) aligned 0 times 543788 (2.31%) aligned exactly 1 time 430470 (1.83%) aligned >1 times 49.39% overall alignment rate Time searching: 00:30:06 Overall time: 00:30:06 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] 1444464 / 10476856 = 0.1379 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 17:42:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.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 17:42:11: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:42:11: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:42:23: 1000000 INFO @ Wed, 08 Dec 2021 17:42:33: 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 17:42:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.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 17:42:41: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:42:41: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:42:45: 3000000 INFO @ Wed, 08 Dec 2021 17:42:57: 1000000 INFO @ Wed, 08 Dec 2021 17:43:05: 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 17:43:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.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 17:43:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:43:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:43:20: 2000000 INFO @ Wed, 08 Dec 2021 17:43:24: 5000000 INFO @ Wed, 08 Dec 2021 17:43:27: 1000000 INFO @ Wed, 08 Dec 2021 17:43:34: 3000000 INFO @ Wed, 08 Dec 2021 17:43:36: 6000000 INFO @ Wed, 08 Dec 2021 17:43:40: 2000000 INFO @ Wed, 08 Dec 2021 17:43:46: 4000000 INFO @ Wed, 08 Dec 2021 17:43:49: 7000000 INFO @ Wed, 08 Dec 2021 17:43:52: 3000000 INFO @ Wed, 08 Dec 2021 17:43:58: 5000000 INFO @ Wed, 08 Dec 2021 17:44:01: 8000000 INFO @ Wed, 08 Dec 2021 17:44:05: 4000000 INFO @ Wed, 08 Dec 2021 17:44:11: 6000000 INFO @ Wed, 08 Dec 2021 17:44:13: 9000000 INFO @ Wed, 08 Dec 2021 17:44:18: 5000000 INFO @ Wed, 08 Dec 2021 17:44:28: 7000000 INFO @ Wed, 08 Dec 2021 17:44:30: 10000000 INFO @ Wed, 08 Dec 2021 17:44:36: 6000000 INFO @ Wed, 08 Dec 2021 17:44:43: 8000000 INFO @ Wed, 08 Dec 2021 17:44:45: 11000000 INFO @ Wed, 08 Dec 2021 17:44:50: 7000000 INFO @ Wed, 08 Dec 2021 17:44:59: 9000000 INFO @ Wed, 08 Dec 2021 17:45:00: 12000000 INFO @ Wed, 08 Dec 2021 17:45:05: 8000000 INFO @ Wed, 08 Dec 2021 17:45:10: 10000000 INFO @ Wed, 08 Dec 2021 17:45:13: 13000000 INFO @ Wed, 08 Dec 2021 17:45:17: 9000000 INFO @ Wed, 08 Dec 2021 17:45:22: 11000000 INFO @ Wed, 08 Dec 2021 17:45:24: 14000000 INFO @ Wed, 08 Dec 2021 17:45:28: 10000000 INFO @ Wed, 08 Dec 2021 17:45:34: 12000000 INFO @ Wed, 08 Dec 2021 17:45:35: 15000000 INFO @ Wed, 08 Dec 2021 17:45:39: 11000000 INFO @ Wed, 08 Dec 2021 17:45:46: 13000000 INFO @ Wed, 08 Dec 2021 17:45:47: 16000000 INFO @ Wed, 08 Dec 2021 17:45:53: 12000000 INFO @ Wed, 08 Dec 2021 17:45:58: 14000000 INFO @ Wed, 08 Dec 2021 17:45:58: 17000000 INFO @ Wed, 08 Dec 2021 17:46:06: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:46:11: 18000000 INFO @ Wed, 08 Dec 2021 17:46:11: 15000000 INFO @ Wed, 08 Dec 2021 17:46:19: 14000000 INFO @ Wed, 08 Dec 2021 17:46:23: 19000000 INFO @ Wed, 08 Dec 2021 17:46:23: 16000000 INFO @ Wed, 08 Dec 2021 17:46:24: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:46:24: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:46:24: #1 total tags in treatment: 6912229 INFO @ Wed, 08 Dec 2021 17:46:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:46:24: #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 17:46:24: #1 tags after filtering in treatment: 6455792 INFO @ Wed, 08 Dec 2021 17:46:24: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:46:24: #1 finished! INFO @ Wed, 08 Dec 2021 17:46:24: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:46:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:46:25: #2 number of paired peaks: 1437 INFO @ Wed, 08 Dec 2021 17:46:25: start model_add_line... INFO @ Wed, 08 Dec 2021 17:46:25: start X-correlation... INFO @ Wed, 08 Dec 2021 17:46:25: end of X-cor INFO @ Wed, 08 Dec 2021 17:46:25: #2 finished! INFO @ Wed, 08 Dec 2021 17:46:25: #2 predicted fragment length is 247 bps INFO @ Wed, 08 Dec 2021 17:46:25: #2 alternative fragment length(s) may be 247 bps INFO @ Wed, 08 Dec 2021 17:46:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.05_model.r WARNING @ Wed, 08 Dec 2021 17:46:25: #2 Since the d (247) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:46:25: #2 You may need to consider one of the other alternative d(s): 247 WARNING @ Wed, 08 Dec 2021 17:46:25: #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 17:46:25: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:46:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:46:31: 15000000 INFO @ Wed, 08 Dec 2021 17:46:35: 17000000 INFO @ Wed, 08 Dec 2021 17:46:42: 16000000 INFO @ Wed, 08 Dec 2021 17:46:47: 18000000 INFO @ Wed, 08 Dec 2021 17:46:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:46:53: 17000000 INFO @ Wed, 08 Dec 2021 17:46:59: 19000000 INFO @ Wed, 08 Dec 2021 17:47:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:47:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:47:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.05_summits.bed INFO @ Wed, 08 Dec 2021 17:47:01: Done! INFO @ Wed, 08 Dec 2021 17:47:01: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:47:01: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:47:01: #1 total tags in treatment: 6912229 INFO @ Wed, 08 Dec 2021 17:47:01: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:47:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3057 records, 4 fields): 6 millis INFO @ Wed, 08 Dec 2021 17:47:01: #1 tags after filtering in treatment: 6455792 INFO @ Wed, 08 Dec 2021 17:47:01: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:47:01: #1 finished! INFO @ Wed, 08 Dec 2021 17:47:01: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:47:01: #2 looking for paired plus/minus strand peaks... CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:47:02: #2 number of paired peaks: 1437 INFO @ Wed, 08 Dec 2021 17:47:02: start model_add_line... INFO @ Wed, 08 Dec 2021 17:47:02: start X-correlation... INFO @ Wed, 08 Dec 2021 17:47:02: end of X-cor INFO @ Wed, 08 Dec 2021 17:47:02: #2 finished! INFO @ Wed, 08 Dec 2021 17:47:02: #2 predicted fragment length is 247 bps INFO @ Wed, 08 Dec 2021 17:47:02: #2 alternative fragment length(s) may be 247 bps INFO @ Wed, 08 Dec 2021 17:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.10_model.r WARNING @ Wed, 08 Dec 2021 17:47:02: #2 Since the d (247) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:47:02: #2 You may need to consider one of the other alternative d(s): 247 WARNING @ Wed, 08 Dec 2021 17:47:02: #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 17:47:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:47:06: 18000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 17:47:18: 19000000 INFO @ Wed, 08 Dec 2021 17:47:20: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:47:20: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:47:20: #1 total tags in treatment: 6912229 INFO @ Wed, 08 Dec 2021 17:47:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:47:20: #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 17:47:20: #1 tags after filtering in treatment: 6455792 INFO @ Wed, 08 Dec 2021 17:47:20: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:47:20: #1 finished! INFO @ Wed, 08 Dec 2021 17:47:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:47:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:47:21: #2 number of paired peaks: 1437 INFO @ Wed, 08 Dec 2021 17:47:21: start model_add_line... INFO @ Wed, 08 Dec 2021 17:47:21: start X-correlation... INFO @ Wed, 08 Dec 2021 17:47:21: end of X-cor INFO @ Wed, 08 Dec 2021 17:47:21: #2 finished! INFO @ Wed, 08 Dec 2021 17:47:21: #2 predicted fragment length is 247 bps INFO @ Wed, 08 Dec 2021 17:47:21: #2 alternative fragment length(s) may be 247 bps INFO @ Wed, 08 Dec 2021 17:47:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.20_model.r WARNING @ Wed, 08 Dec 2021 17:47:21: #2 Since the d (247) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:47:21: #2 You may need to consider one of the other alternative d(s): 247 WARNING @ Wed, 08 Dec 2021 17:47:21: #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 17:47:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:47:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:47:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:47:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.10_peaks.xls INFO @ Wed, 08 Dec 2021 17:47:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:47:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.10_summits.bed INFO @ Wed, 08 Dec 2021 17:47:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1338 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:47:46: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:47:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.20_peaks.xls INFO @ Wed, 08 Dec 2021 17:47:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:47:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641181/SRX10641181.20_summits.bed INFO @ Wed, 08 Dec 2021 17:47:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (463 records, 4 fields): 2 millis CompletedMACS2peakCalling