[2024-01-25 19:07:50,589] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:50,590] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:50,591] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f577081-c6f9-409d-8e6e-a9cb32213271/dqc_reference
[2024-01-25 19:07:51,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:51,819] [INFO] Task started: Prodigal
[2024-01-25 19:07:51,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fc5cf2a-3d49-450c-b6fb-e8c7d97ae271/GCF_003646465.1_ASM364646v1_genomic.fna.gz | prodigal -d GCF_003646465.1_ASM364646v1_genomic.fna/cds.fna -a GCF_003646465.1_ASM364646v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:08:05,199] [INFO] Task succeeded: Prodigal
[2024-01-25 19:08:05,199] [INFO] Task started: HMMsearch
[2024-01-25 19:08:05,199] [INFO] Running command: hmmsearch --tblout GCF_003646465.1_ASM364646v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f577081-c6f9-409d-8e6e-a9cb32213271/dqc_reference/reference_markers.hmm GCF_003646465.1_ASM364646v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:08:05,500] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:08:05,502] [INFO] Found 6/6 markers.
[2024-01-25 19:08:05,547] [INFO] Query marker FASTA was written to GCF_003646465.1_ASM364646v1_genomic.fna/markers.fasta
[2024-01-25 19:08:05,548] [INFO] Task started: Blastn
[2024-01-25 19:08:05,548] [INFO] Running command: blastn -query GCF_003646465.1_ASM364646v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f577081-c6f9-409d-8e6e-a9cb32213271/dqc_reference/reference_markers.fasta -out GCF_003646465.1_ASM364646v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:06,360] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:06,362] [INFO] Selected 28 target genomes.
[2024-01-25 19:08:06,363] [INFO] Target genome list was writen to GCF_003646465.1_ASM364646v1_genomic.fna/target_genomes.txt
[2024-01-25 19:08:06,386] [INFO] Task started: fastANI
[2024-01-25 19:08:06,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fc5cf2a-3d49-450c-b6fb-e8c7d97ae271/GCF_003646465.1_ASM364646v1_genomic.fna.gz --refList GCF_003646465.1_ASM364646v1_genomic.fna/target_genomes.txt --output GCF_003646465.1_ASM364646v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:30,232] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:30,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f577081-c6f9-409d-8e6e-a9cb32213271/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:30,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f577081-c6f9-409d-8e6e-a9cb32213271/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:30,249] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:08:30,249] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:08:30,249] [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
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	82.0122	976	1658	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.938	534	1658	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.8134	533	1658	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.8092	572	1658	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.7361	458	1658	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.7356	531	1658	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.6991	484	1658	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.6456	500	1658	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.63	553	1658	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.6282	489	1658	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.5997	559	1658	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	78.5872	448	1658	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.5276	471	1658	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	78.5219	445	1658	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	78.4204	486	1658	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.3461	406	1658	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.3198	528	1658	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.2719	387	1658	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.206	489	1658	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	78.1841	490	1658	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	78.1416	430	1658	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.9711	382	1658	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.9193	369	1658	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	77.8854	445	1658	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.8821	335	1658	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	77.7314	275	1658	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.6324	365	1658	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	77.5604	353	1658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:30,250] [INFO] DFAST Taxonomy check result was written to GCF_003646465.1_ASM364646v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:30,251] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:30,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:30,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f577081-c6f9-409d-8e6e-a9cb32213271/dqc_reference/checkm_data
[2024-01-25 19:08:30,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:30,300] [INFO] Task started: CheckM
[2024-01-25 19:08:30,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003646465.1_ASM364646v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003646465.1_ASM364646v1_genomic.fna/checkm_input GCF_003646465.1_ASM364646v1_genomic.fna/checkm_result
[2024-01-25 19:09:13,316] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:13,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:13,339] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:13,339] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:13,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003646465.1_ASM364646v1_genomic.fna/markers.fasta)
[2024-01-25 19:09:13,339] [INFO] Task started: Blastn
[2024-01-25 19:09:13,339] [INFO] Running command: blastn -query GCF_003646465.1_ASM364646v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f577081-c6f9-409d-8e6e-a9cb32213271/dqc_reference/reference_markers_gtdb.fasta -out GCF_003646465.1_ASM364646v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:14,731] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:14,736] [INFO] Selected 20 target genomes.
[2024-01-25 19:09:14,737] [INFO] Target genome list was writen to GCF_003646465.1_ASM364646v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:14,763] [INFO] Task started: fastANI
[2024-01-25 19:09:14,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fc5cf2a-3d49-450c-b6fb-e8c7d97ae271/GCF_003646465.1_ASM364646v1_genomic.fna.gz --refList GCF_003646465.1_ASM364646v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003646465.1_ASM364646v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:33,604] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:33,616] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:33,616] [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
GCF_003646465.1	s__Chachezhania antarctica	100.0	1655	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009765275.1	s__Chachezhania sp009765275	82.0382	972	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210095.1	s__Marinibacterium profundimaris	80.3824	756	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	80.0861	741	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	79.7845	615	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	79.5617	509	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	79.0234	540	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.7859	578	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	78.7235	541	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	78.7097	511	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.6911	485	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938225.1	s__Arenibacterium halophilum	78.6704	560	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_005938215.1	s__Ruegeria sediminis	78.6455	487	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	78.6452	500	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.6145	556	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900108275.1	s__Jhaorihella thermophila	78.4236	500	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	77.9802	323	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116005.1	s__Poseidonocella sedimentorum	77.8736	341	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216475.1	s__GCA-004216475 sp004216475	77.7722	356	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-004216475	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030985.1	s__Ruegeria arenilitoris_B	77.5216	385	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:33,618] [INFO] GTDB search result was written to GCF_003646465.1_ASM364646v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:33,619] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:33,623] [INFO] DFAST_QC result json was written to GCF_003646465.1_ASM364646v1_genomic.fna/dqc_result.json
[2024-01-25 19:09:33,623] [INFO] DFAST_QC completed!
[2024-01-25 19:09:33,623] [INFO] Total running time: 0h1m43s