Job ID = 14159479 SRX = SRX8845623 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6657807 spots for SRR12345968/SRR12345968.sra Written 6657807 spots for SRR12345968/SRR12345968.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159659 ("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: 00:05:47 6657807 reads; of these: 6657807 (100.00%) were paired; of these: 2130792 (32.00%) aligned concordantly 0 times 4014618 (60.30%) aligned concordantly exactly 1 time 512397 (7.70%) aligned concordantly >1 times ---- 2130792 pairs aligned concordantly 0 times; of these: 850565 (39.92%) aligned discordantly 1 time ---- 1280227 pairs aligned 0 times concordantly or discordantly; of these: 2560454 mates make up the pairs; of these: 2144649 (83.76%) aligned 0 times 215943 (8.43%) aligned exactly 1 time 199862 (7.81%) aligned >1 times 83.89% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 847078 / 5323841 = 0.1591 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 22:15:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.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 22:15:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:15:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:16:00: 1000000 INFO @ Wed, 08 Dec 2021 22:16:04: 2000000 INFO @ Wed, 08 Dec 2021 22:16:09: 3000000 INFO @ Wed, 08 Dec 2021 22:16:14: 4000000 INFO @ Wed, 08 Dec 2021 22:16:18: 5000000 INFO @ Wed, 08 Dec 2021 22:16:23: 6000000 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 22:16:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.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 22:16:25: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:16:25: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:16:27: 7000000 INFO @ Wed, 08 Dec 2021 22:16:30: 1000000 INFO @ Wed, 08 Dec 2021 22:16:32: 8000000 INFO @ Wed, 08 Dec 2021 22:16:35: 2000000 INFO @ Wed, 08 Dec 2021 22:16:37: 9000000 INFO @ Wed, 08 Dec 2021 22:16:39: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:16:39: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:16:39: #1 total tags in treatment: 3821357 INFO @ Wed, 08 Dec 2021 22:16:39: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:16:39: #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 22:16:39: #1 tags after filtering in treatment: 2736191 INFO @ Wed, 08 Dec 2021 22:16:39: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 08 Dec 2021 22:16:39: #1 finished! INFO @ Wed, 08 Dec 2021 22:16:39: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:16:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:16:39: 3000000 INFO @ Wed, 08 Dec 2021 22:16:39: #2 number of paired peaks: 4186 INFO @ Wed, 08 Dec 2021 22:16:39: start model_add_line... INFO @ Wed, 08 Dec 2021 22:16:39: start X-correlation... INFO @ Wed, 08 Dec 2021 22:16:39: end of X-cor INFO @ Wed, 08 Dec 2021 22:16:39: #2 finished! INFO @ Wed, 08 Dec 2021 22:16:39: #2 predicted fragment length is 113 bps INFO @ Wed, 08 Dec 2021 22:16:39: #2 alternative fragment length(s) may be 113 bps INFO @ Wed, 08 Dec 2021 22:16:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.05_model.r WARNING @ Wed, 08 Dec 2021 22:16:39: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:16:39: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Wed, 08 Dec 2021 22:16:39: #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 22:16:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:16:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:16:44: 4000000 INFO @ Wed, 08 Dec 2021 22:16:45: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:16:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:16:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:16:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.05_summits.bed INFO @ Wed, 08 Dec 2021 22:16:48: Done! INFO @ Wed, 08 Dec 2021 22:16:48: 5000000 pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8422 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:16:53: 6000000 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 22:16:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.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 22:16:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:16:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:16:58: 7000000 INFO @ Wed, 08 Dec 2021 22:17:01: 1000000 INFO @ Wed, 08 Dec 2021 22:17:02: 8000000 INFO @ Wed, 08 Dec 2021 22:17:07: 2000000 INFO @ Wed, 08 Dec 2021 22:17:07: 9000000 INFO @ Wed, 08 Dec 2021 22:17:09: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:17:09: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:17:09: #1 total tags in treatment: 3821357 INFO @ Wed, 08 Dec 2021 22:17:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:17:09: #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 22:17:09: #1 tags after filtering in treatment: 2736191 INFO @ Wed, 08 Dec 2021 22:17:09: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 08 Dec 2021 22:17:09: #1 finished! INFO @ Wed, 08 Dec 2021 22:17:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:17:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:17:10: #2 number of paired peaks: 4186 INFO @ Wed, 08 Dec 2021 22:17:10: start model_add_line... INFO @ Wed, 08 Dec 2021 22:17:10: start X-correlation... INFO @ Wed, 08 Dec 2021 22:17:10: end of X-cor INFO @ Wed, 08 Dec 2021 22:17:10: #2 finished! INFO @ Wed, 08 Dec 2021 22:17:10: #2 predicted fragment length is 113 bps INFO @ Wed, 08 Dec 2021 22:17:10: #2 alternative fragment length(s) may be 113 bps INFO @ Wed, 08 Dec 2021 22:17:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.10_model.r WARNING @ Wed, 08 Dec 2021 22:17:10: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:17:10: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Wed, 08 Dec 2021 22:17:10: #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 22:17:10: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:17:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:17:12: 3000000 INFO @ Wed, 08 Dec 2021 22:17:16: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:17:18: 4000000 INFO @ Wed, 08 Dec 2021 22:17:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:17:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:17:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.10_summits.bed INFO @ Wed, 08 Dec 2021 22:17:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5391 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:17:23: 5000000 INFO @ Wed, 08 Dec 2021 22:17:28: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:17:34: 7000000 INFO @ Wed, 08 Dec 2021 22:17:40: 8000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:17:45: 9000000 INFO @ Wed, 08 Dec 2021 22:17:48: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:17:48: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:17:48: #1 total tags in treatment: 3821357 INFO @ Wed, 08 Dec 2021 22:17:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:17:48: #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 22:17:48: #1 tags after filtering in treatment: 2736191 INFO @ Wed, 08 Dec 2021 22:17:48: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 08 Dec 2021 22:17:48: #1 finished! INFO @ Wed, 08 Dec 2021 22:17:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:17:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:17:48: #2 number of paired peaks: 4186 INFO @ Wed, 08 Dec 2021 22:17:48: start model_add_line... INFO @ Wed, 08 Dec 2021 22:17:49: start X-correlation... INFO @ Wed, 08 Dec 2021 22:17:49: end of X-cor INFO @ Wed, 08 Dec 2021 22:17:49: #2 finished! INFO @ Wed, 08 Dec 2021 22:17:49: #2 predicted fragment length is 113 bps INFO @ Wed, 08 Dec 2021 22:17:49: #2 alternative fragment length(s) may be 113 bps INFO @ Wed, 08 Dec 2021 22:17:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.20_model.r WARNING @ Wed, 08 Dec 2021 22:17:49: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:17:49: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Wed, 08 Dec 2021 22:17:49: #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 22:17:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:17:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:17:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:17:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:17:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:17:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845623/SRX8845623.20_summits.bed INFO @ Wed, 08 Dec 2021 22:17:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2867 records, 4 fields): 4 millis CompletedMACS2peakCalling