[2024-01-25 18:08:05,703] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:05,704] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:05,705] [INFO] DQC Reference Directory: /var/lib/cwl/stg33f3a03f-eb92-4166-96fb-32f0c5856106/dqc_reference
[2024-01-25 18:08:06,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:06,860] [INFO] Task started: Prodigal
[2024-01-25 18:08:06,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c397e27-7d18-49f4-9fcf-4abe30bab515/GCF_003258355.1_ASM325835v1_genomic.fna.gz | prodigal -d GCF_003258355.1_ASM325835v1_genomic.fna/cds.fna -a GCF_003258355.1_ASM325835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:18,894] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:18,895] [INFO] Task started: HMMsearch
[2024-01-25 18:08:18,895] [INFO] Running command: hmmsearch --tblout GCF_003258355.1_ASM325835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33f3a03f-eb92-4166-96fb-32f0c5856106/dqc_reference/reference_markers.hmm GCF_003258355.1_ASM325835v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:19,143] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:19,144] [INFO] Found 6/6 markers.
[2024-01-25 18:08:19,177] [INFO] Query marker FASTA was written to GCF_003258355.1_ASM325835v1_genomic.fna/markers.fasta
[2024-01-25 18:08:19,177] [INFO] Task started: Blastn
[2024-01-25 18:08:19,178] [INFO] Running command: blastn -query GCF_003258355.1_ASM325835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33f3a03f-eb92-4166-96fb-32f0c5856106/dqc_reference/reference_markers.fasta -out GCF_003258355.1_ASM325835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:19,900] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:19,904] [INFO] Selected 13 target genomes.
[2024-01-25 18:08:19,904] [INFO] Target genome list was writen to GCF_003258355.1_ASM325835v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:19,913] [INFO] Task started: fastANI
[2024-01-25 18:08:19,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c397e27-7d18-49f4-9fcf-4abe30bab515/GCF_003258355.1_ASM325835v1_genomic.fna.gz --refList GCF_003258355.1_ASM325835v1_genomic.fna/target_genomes.txt --output GCF_003258355.1_ASM325835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:28,970] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:28,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33f3a03f-eb92-4166-96fb-32f0c5856106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:28,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33f3a03f-eb92-4166-96fb-32f0c5856106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:28,979] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:28,979] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:28,979] [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
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	100.0	1345	1348	95	conclusive
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	82.0395	730	1348	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	81.8532	712	1348	95	below_threshold
Confluentibacter citreus	strain=XJNY	GCA_002807055.1	2007307	2007307	type	True	81.7501	728	1348	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.7704	480	1348	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.1916	350	1348	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	78.1082	379	1348	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.0381	348	1348	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.4939	216	1348	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.3816	215	1348	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.3545	219	1348	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.338	265	1348	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.2968	190	1348	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:28,980] [INFO] DFAST Taxonomy check result was written to GCF_003258355.1_ASM325835v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:28,981] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:28,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:28,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33f3a03f-eb92-4166-96fb-32f0c5856106/dqc_reference/checkm_data
[2024-01-25 18:08:28,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:29,025] [INFO] Task started: CheckM
[2024-01-25 18:08:29,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003258355.1_ASM325835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003258355.1_ASM325835v1_genomic.fna/checkm_input GCF_003258355.1_ASM325835v1_genomic.fna/checkm_result
[2024-01-25 18:09:05,560] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:05,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:05,578] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:05,579] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:05,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003258355.1_ASM325835v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:05,579] [INFO] Task started: Blastn
[2024-01-25 18:09:05,579] [INFO] Running command: blastn -query GCF_003258355.1_ASM325835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33f3a03f-eb92-4166-96fb-32f0c5856106/dqc_reference/reference_markers_gtdb.fasta -out GCF_003258355.1_ASM325835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:06,594] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:06,597] [INFO] Selected 8 target genomes.
[2024-01-25 18:09:06,597] [INFO] Target genome list was writen to GCF_003258355.1_ASM325835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:06,610] [INFO] Task started: fastANI
[2024-01-25 18:09:06,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c397e27-7d18-49f4-9fcf-4abe30bab515/GCF_003258355.1_ASM325835v1_genomic.fna.gz --refList GCF_003258355.1_ASM325835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003258355.1_ASM325835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:13,197] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:13,204] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:13,204] [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_003258355.1	s__Confluentibacter sp003258355	100.0	1345	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002843175.1	s__Confluentibacter flavum	82.0372	730	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806995.1	s__Confluentibacter lentus	81.8472	713	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807055.1	s__Confluentibacter citreus	81.7606	727	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280395.1	s__Confluentibacter sp002280395	81.3706	405	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.7704	480	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	78.1277	377	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.0503	346	1348	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:13,205] [INFO] GTDB search result was written to GCF_003258355.1_ASM325835v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:13,206] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:13,209] [INFO] DFAST_QC result json was written to GCF_003258355.1_ASM325835v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:13,209] [INFO] DFAST_QC completed!
[2024-01-25 18:09:13,209] [INFO] Total running time: 0h1m8s