Job ID = 14158389 SRX = SRX10641183 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-08T07:53:37 prefetch.2.10.7: 1) Downloading 'SRR14280095'... 2021-12-08T07:53:37 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T08:03:47 prefetch.2.10.7: HTTPS download succeed 2021-12-08T08:03:47 prefetch.2.10.7: 1) 'SRR14280095' was downloaded successfully 2021-12-08T08:03:47 prefetch.2.10.7: 'SRR14280095' has 0 unresolved dependencies Read 18512901 spots for SRR14280095/SRR14280095.sra Written 18512901 spots for SRR14280095/SRR14280095.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159085 ("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: 00:26:19 18512901 reads; of these: 18512901 (100.00%) were paired; of these: 12019104 (64.92%) aligned concordantly 0 times 5801740 (31.34%) aligned concordantly exactly 1 time 692057 (3.74%) aligned concordantly >1 times ---- 12019104 pairs aligned concordantly 0 times; of these: 2263228 (18.83%) aligned discordantly 1 time ---- 9755876 pairs aligned 0 times concordantly or discordantly; of these: 19511752 mates make up the pairs; of these: 18546634 (95.05%) aligned 0 times 544113 (2.79%) aligned exactly 1 time 421005 (2.16%) aligned >1 times 49.91% overall alignment rate Time searching: 00:26:19 Overall time: 00:26:19 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] 1110785 / 8729343 = 0.1272 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 17:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.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 17:47:11: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:47:11: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:47:23: 1000000 INFO @ Wed, 08 Dec 2021 17:47:36: 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 17:47:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.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 17:47:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:47:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:47:49: 3000000 INFO @ Wed, 08 Dec 2021 17:47:54: 1000000 INFO @ Wed, 08 Dec 2021 17:48:00: 4000000 INFO @ Wed, 08 Dec 2021 17:48:06: 2000000 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 17:48:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.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 17:48:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:48:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:48:12: 5000000 INFO @ Wed, 08 Dec 2021 17:48:20: 3000000 INFO @ Wed, 08 Dec 2021 17:48:26: 1000000 INFO @ Wed, 08 Dec 2021 17:48:26: 6000000 INFO @ Wed, 08 Dec 2021 17:48:33: 4000000 INFO @ Wed, 08 Dec 2021 17:48:39: 7000000 INFO @ Wed, 08 Dec 2021 17:48:41: 2000000 INFO @ Wed, 08 Dec 2021 17:48:47: 5000000 INFO @ Wed, 08 Dec 2021 17:48:52: 8000000 INFO @ Wed, 08 Dec 2021 17:48:56: 3000000 INFO @ Wed, 08 Dec 2021 17:49:00: 6000000 INFO @ Wed, 08 Dec 2021 17:49:05: 9000000 INFO @ Wed, 08 Dec 2021 17:49:11: 4000000 INFO @ Wed, 08 Dec 2021 17:49:14: 7000000 INFO @ Wed, 08 Dec 2021 17:49:19: 10000000 INFO @ Wed, 08 Dec 2021 17:49:27: 5000000 INFO @ Wed, 08 Dec 2021 17:49:27: 8000000 INFO @ Wed, 08 Dec 2021 17:49:33: 11000000 INFO @ Wed, 08 Dec 2021 17:49:41: 9000000 INFO @ Wed, 08 Dec 2021 17:49:42: 6000000 INFO @ Wed, 08 Dec 2021 17:49:47: 12000000 INFO @ Wed, 08 Dec 2021 17:49:55: 10000000 INFO @ Wed, 08 Dec 2021 17:49:58: 7000000 INFO @ Wed, 08 Dec 2021 17:50:01: 13000000 INFO @ Wed, 08 Dec 2021 17:50:09: 11000000 INFO @ Wed, 08 Dec 2021 17:50:13: 8000000 INFO @ Wed, 08 Dec 2021 17:50:15: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:50:22: 12000000 INFO @ Wed, 08 Dec 2021 17:50:28: 15000000 INFO @ Wed, 08 Dec 2021 17:50:29: 9000000 INFO @ Wed, 08 Dec 2021 17:50:37: 13000000 INFO @ Wed, 08 Dec 2021 17:50:41: 16000000 INFO @ Wed, 08 Dec 2021 17:50:44: 10000000 INFO @ Wed, 08 Dec 2021 17:50:45: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:50:45: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:50:45: #1 total tags in treatment: 5606710 INFO @ Wed, 08 Dec 2021 17:50:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:50:45: #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 17:50:45: #1 tags after filtering in treatment: 5279477 INFO @ Wed, 08 Dec 2021 17:50:45: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 17:50:45: #1 finished! INFO @ Wed, 08 Dec 2021 17:50:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:50:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:50:46: #2 number of paired peaks: 1512 INFO @ Wed, 08 Dec 2021 17:50:46: start model_add_line... INFO @ Wed, 08 Dec 2021 17:50:46: start X-correlation... INFO @ Wed, 08 Dec 2021 17:50:46: end of X-cor INFO @ Wed, 08 Dec 2021 17:50:46: #2 finished! INFO @ Wed, 08 Dec 2021 17:50:46: #2 predicted fragment length is 249 bps INFO @ Wed, 08 Dec 2021 17:50:46: #2 alternative fragment length(s) may be 249 bps INFO @ Wed, 08 Dec 2021 17:50:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.05_model.r WARNING @ Wed, 08 Dec 2021 17:50:46: #2 Since the d (249) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:50:46: #2 You may need to consider one of the other alternative d(s): 249 WARNING @ Wed, 08 Dec 2021 17:50:46: #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 17:50:46: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:50:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:50:51: 14000000 INFO @ Wed, 08 Dec 2021 17:50:59: 11000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 17:51:04: 15000000 INFO @ Wed, 08 Dec 2021 17:51:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:51:14: 12000000 INFO @ Wed, 08 Dec 2021 17:51:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:51:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:51:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.05_summits.bed INFO @ Wed, 08 Dec 2021 17:51:16: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1949 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:51:17: 16000000 INFO @ Wed, 08 Dec 2021 17:51:20: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:51:20: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:51:20: #1 total tags in treatment: 5606710 INFO @ Wed, 08 Dec 2021 17:51:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:51:20: #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 17:51:20: #1 tags after filtering in treatment: 5279477 INFO @ Wed, 08 Dec 2021 17:51:20: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 17:51:20: #1 finished! INFO @ Wed, 08 Dec 2021 17:51:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:51:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:51:20: #2 number of paired peaks: 1512 INFO @ Wed, 08 Dec 2021 17:51:20: start model_add_line... INFO @ Wed, 08 Dec 2021 17:51:21: start X-correlation... INFO @ Wed, 08 Dec 2021 17:51:21: end of X-cor INFO @ Wed, 08 Dec 2021 17:51:21: #2 finished! INFO @ Wed, 08 Dec 2021 17:51:21: #2 predicted fragment length is 249 bps INFO @ Wed, 08 Dec 2021 17:51:21: #2 alternative fragment length(s) may be 249 bps INFO @ Wed, 08 Dec 2021 17:51:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.10_model.r WARNING @ Wed, 08 Dec 2021 17:51:21: #2 Since the d (249) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:51:21: #2 You may need to consider one of the other alternative d(s): 249 WARNING @ Wed, 08 Dec 2021 17:51:21: #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 17:51:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:51:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:51:29: 13000000 INFO @ Wed, 08 Dec 2021 17:51:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:51:44: 14000000 INFO @ Wed, 08 Dec 2021 17:51:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.10_peaks.xls INFO @ Wed, 08 Dec 2021 17:51:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:51:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.10_summits.bed INFO @ Wed, 08 Dec 2021 17:51:50: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (833 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:51:59: 15000000 INFO @ Wed, 08 Dec 2021 17:52:13: 16000000 INFO @ Wed, 08 Dec 2021 17:52:17: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:52:17: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:52:17: #1 total tags in treatment: 5606710 INFO @ Wed, 08 Dec 2021 17:52:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:52:17: #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 17:52:17: #1 tags after filtering in treatment: 5279477 INFO @ Wed, 08 Dec 2021 17:52:17: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 17:52:17: #1 finished! INFO @ Wed, 08 Dec 2021 17:52:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:52:17: #2 number of paired peaks: 1512 INFO @ Wed, 08 Dec 2021 17:52:17: start model_add_line... INFO @ Wed, 08 Dec 2021 17:52:17: start X-correlation... INFO @ Wed, 08 Dec 2021 17:52:17: end of X-cor INFO @ Wed, 08 Dec 2021 17:52:17: #2 finished! INFO @ Wed, 08 Dec 2021 17:52:17: #2 predicted fragment length is 249 bps INFO @ Wed, 08 Dec 2021 17:52:17: #2 alternative fragment length(s) may be 249 bps INFO @ Wed, 08 Dec 2021 17:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.20_model.r WARNING @ Wed, 08 Dec 2021 17:52:17: #2 Since the d (249) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:52:17: #2 You may need to consider one of the other alternative d(s): 249 WARNING @ Wed, 08 Dec 2021 17:52:17: #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 17:52:17: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:52:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:52:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.20_peaks.xls INFO @ Wed, 08 Dec 2021 17:52:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:52:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641183/SRX10641183.20_summits.bed INFO @ Wed, 08 Dec 2021 17:52:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (361 records, 4 fields): 4 millis CompletedMACS2peakCalling