[2023-06-19 08:29:50,717] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:29:50,725] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:29:50,725] [INFO] DQC Reference Directory: /var/lib/cwl/stg60d89d78-c6c9-4334-aade-b7b20135313f/dqc_reference
[2023-06-19 08:29:53,044] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:29:53,045] [INFO] Task started: Prodigal
[2023-06-19 08:29:53,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg5362be95-e88a-4c71-b046-da2c7ab2e78e/GCA_013201385.1_ASM1320138v1_genomic.fna.gz | prodigal -d GCA_013201385.1_ASM1320138v1_genomic.fna/cds.fna -a GCA_013201385.1_ASM1320138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:29:58,139] [INFO] Task succeeded: Prodigal
[2023-06-19 08:29:58,139] [INFO] Task started: HMMsearch
[2023-06-19 08:29:58,139] [INFO] Running command: hmmsearch --tblout GCA_013201385.1_ASM1320138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60d89d78-c6c9-4334-aade-b7b20135313f/dqc_reference/reference_markers.hmm GCA_013201385.1_ASM1320138v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:29:58,349] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:29:58,350] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5362be95-e88a-4c71-b046-da2c7ab2e78e/GCA_013201385.1_ASM1320138v1_genomic.fna.gz]
[2023-06-19 08:29:58,379] [INFO] Query marker FASTA was written to GCA_013201385.1_ASM1320138v1_genomic.fna/markers.fasta
[2023-06-19 08:29:58,379] [INFO] Task started: Blastn
[2023-06-19 08:29:58,379] [INFO] Running command: blastn -query GCA_013201385.1_ASM1320138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60d89d78-c6c9-4334-aade-b7b20135313f/dqc_reference/reference_markers.fasta -out GCA_013201385.1_ASM1320138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:29:58,912] [INFO] Task succeeded: Blastn
[2023-06-19 08:29:58,916] [INFO] Selected 8 target genomes.
[2023-06-19 08:29:58,916] [INFO] Target genome list was writen to GCA_013201385.1_ASM1320138v1_genomic.fna/target_genomes.txt
[2023-06-19 08:29:58,920] [INFO] Task started: fastANI
[2023-06-19 08:29:58,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg5362be95-e88a-4c71-b046-da2c7ab2e78e/GCA_013201385.1_ASM1320138v1_genomic.fna.gz --refList GCA_013201385.1_ASM1320138v1_genomic.fna/target_genomes.txt --output GCA_013201385.1_ASM1320138v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:30:03,262] [INFO] Task succeeded: fastANI
[2023-06-19 08:30:03,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60d89d78-c6c9-4334-aade-b7b20135313f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:30:03,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60d89d78-c6c9-4334-aade-b7b20135313f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:30:03,271] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:30:03,271] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:30:03,271] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Methanoculleus bourgensis	strain=MS2T	GCA_000304355.2	83986	83986	type	True	85.4492	438	561	95	below_threshold
Methanoculleus marisnigri	strain=JR1	GCA_000015825.1	2198	2198	type	True	80.7907	326	561	95	below_threshold
Methanoculleus sediminis	strain=S3Fa	GCA_001017125.1	1550566	1550566	type	True	80.5367	323	561	95	below_threshold
Methanoculleus chikugoensis	strain=MG62	GCA_019669965.1	118126	118126	type	True	80.4186	345	561	95	below_threshold
Methanoculleus horonobensis	strain=T10	GCA_001602375.1	528314	528314	type	True	80.3951	333	561	95	below_threshold
Methanoculleus chikugoensis	strain=JCM 10825	GCA_001315965.1	118126	118126	type	True	80.0731	299	561	95	below_threshold
Methanoculleus thermophilus	strain=CR-1	GCA_001571405.1	2200	2200	type	True	79.6473	275	561	95	below_threshold
Methanoculleus thermophilus	strain=DSM 2373	GCA_900101055.1	2200	2200	type	True	79.6358	276	561	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:30:03,273] [INFO] DFAST Taxonomy check result was written to GCA_013201385.1_ASM1320138v1_genomic.fna/tc_result.tsv
[2023-06-19 08:30:03,274] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:30:03,274] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:30:03,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60d89d78-c6c9-4334-aade-b7b20135313f/dqc_reference/checkm_data
[2023-06-19 08:30:03,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:30:03,303] [INFO] Task started: CheckM
[2023-06-19 08:30:03,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013201385.1_ASM1320138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013201385.1_ASM1320138v1_genomic.fna/checkm_input GCA_013201385.1_ASM1320138v1_genomic.fna/checkm_result
[2023-06-19 08:30:25,175] [INFO] Task succeeded: CheckM
[2023-06-19 08:30:25,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.61%
Contamintation: 12.50%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2023-06-19 08:30:25,207] [INFO] ===== Completeness check finished =====
[2023-06-19 08:30:25,207] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:30:25,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013201385.1_ASM1320138v1_genomic.fna/markers.fasta)
[2023-06-19 08:30:25,208] [INFO] Task started: Blastn
[2023-06-19 08:30:25,208] [INFO] Running command: blastn -query GCA_013201385.1_ASM1320138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60d89d78-c6c9-4334-aade-b7b20135313f/dqc_reference/reference_markers_gtdb.fasta -out GCA_013201385.1_ASM1320138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:30:25,697] [INFO] Task succeeded: Blastn
[2023-06-19 08:30:25,702] [INFO] Selected 8 target genomes.
[2023-06-19 08:30:25,702] [INFO] Target genome list was writen to GCA_013201385.1_ASM1320138v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:30:25,708] [INFO] Task started: fastANI
[2023-06-19 08:30:25,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg5362be95-e88a-4c71-b046-da2c7ab2e78e/GCA_013201385.1_ASM1320138v1_genomic.fna.gz --refList GCA_013201385.1_ASM1320138v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013201385.1_ASM1320138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:30:29,524] [INFO] Task succeeded: fastANI
[2023-06-19 08:30:29,536] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:30:29,537] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_012797575.1	s__Methanoculleus sp012797575	98.1756	340	561	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	98.26	98.26	0.78	0.78	2	conclusive
GCF_000304355.2	s__Methanoculleus bourgensis	85.4837	437	561	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	96.25	95.89	0.90	0.87	7	-
GCA_001512375.1	s__Methanoculleus thermohydrogenotrophicum	83.0785	335	561	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	99.70	99.65	0.89	0.87	3	-
GCA_012510335.1	s__Methanoculleus sp012510335	82.208	245	561	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521035.1	s__Methanoculleus sp012521035	82.1665	300	561	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012510295.1	s__Methanoculleus sp012510295	81.907	228	561	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001896715.1	s__Methanoculleus sp001896715	81.0577	245	561	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	98.35	97.95	0.73	0.67	3	-
GCA_016841955.1	s__Methanoculleus sp016841955	81.019	345	561	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	99.79	99.79	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-19 08:30:29,540] [INFO] GTDB search result was written to GCA_013201385.1_ASM1320138v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:30:29,541] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:30:29,545] [INFO] DFAST_QC result json was written to GCA_013201385.1_ASM1320138v1_genomic.fna/dqc_result.json
[2023-06-19 08:30:29,545] [INFO] DFAST_QC completed!
[2023-06-19 08:30:29,546] [INFO] Total running time: 0h0m39s