[2024-01-25 20:01:21,151] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:21,152] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:21,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg847af0a5-932d-43ac-9b16-96ba12a63055/dqc_reference
[2024-01-25 20:01:22,298] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:22,299] [INFO] Task started: Prodigal
[2024-01-25 20:01:22,300] [INFO] Running command: gunzip -c /var/lib/cwl/stg44f5c997-357b-4596-88d0-60481020db33/GCF_003298775.1_ASM329877v1_genomic.fna.gz | prodigal -d GCF_003298775.1_ASM329877v1_genomic.fna/cds.fna -a GCF_003298775.1_ASM329877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:31,582] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:31,582] [INFO] Task started: HMMsearch
[2024-01-25 20:01:31,582] [INFO] Running command: hmmsearch --tblout GCF_003298775.1_ASM329877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg847af0a5-932d-43ac-9b16-96ba12a63055/dqc_reference/reference_markers.hmm GCF_003298775.1_ASM329877v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:31,799] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:31,802] [INFO] Found 6/6 markers.
[2024-01-25 20:01:31,831] [INFO] Query marker FASTA was written to GCF_003298775.1_ASM329877v1_genomic.fna/markers.fasta
[2024-01-25 20:01:31,831] [INFO] Task started: Blastn
[2024-01-25 20:01:31,831] [INFO] Running command: blastn -query GCF_003298775.1_ASM329877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg847af0a5-932d-43ac-9b16-96ba12a63055/dqc_reference/reference_markers.fasta -out GCF_003298775.1_ASM329877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:32,852] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:32,855] [INFO] Selected 29 target genomes.
[2024-01-25 20:01:32,855] [INFO] Target genome list was writen to GCF_003298775.1_ASM329877v1_genomic.fna/target_genomes.txt
[2024-01-25 20:01:32,889] [INFO] Task started: fastANI
[2024-01-25 20:01:32,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f5c997-357b-4596-88d0-60481020db33/GCF_003298775.1_ASM329877v1_genomic.fna.gz --refList GCF_003298775.1_ASM329877v1_genomic.fna/target_genomes.txt --output GCF_003298775.1_ASM329877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:55,758] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:55,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg847af0a5-932d-43ac-9b16-96ba12a63055/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:55,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg847af0a5-932d-43ac-9b16-96ba12a63055/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:55,774] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:01:55,774] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:01:55,775] [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
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.5573	606	1267	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.5052	554	1267	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	79.0903	558	1267	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	78.9922	512	1267	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	78.9893	511	1267	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	78.9656	557	1267	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.9641	583	1267	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.8489	498	1267	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.8406	535	1267	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.8002	533	1267	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	78.7946	525	1267	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.7874	474	1267	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.7348	514	1267	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.7251	485	1267	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.7107	532	1267	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.6526	459	1267	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.6161	474	1267	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5655	491	1267	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	78.5399	493	1267	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.3386	528	1267	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.3208	537	1267	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.3023	521	1267	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	78.1699	429	1267	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.0947	397	1267	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	78.0469	416	1267	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	77.9426	399	1267	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.886	403	1267	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	77.8666	430	1267	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.6488	414	1267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:55,776] [INFO] DFAST Taxonomy check result was written to GCF_003298775.1_ASM329877v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:55,776] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:55,777] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:55,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg847af0a5-932d-43ac-9b16-96ba12a63055/dqc_reference/checkm_data
[2024-01-25 20:01:55,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:55,817] [INFO] Task started: CheckM
[2024-01-25 20:01:55,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003298775.1_ASM329877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003298775.1_ASM329877v1_genomic.fna/checkm_input GCF_003298775.1_ASM329877v1_genomic.fna/checkm_result
[2024-01-25 20:02:41,797] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:41,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:41,815] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:41,815] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:41,816] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003298775.1_ASM329877v1_genomic.fna/markers.fasta)
[2024-01-25 20:02:41,817] [INFO] Task started: Blastn
[2024-01-25 20:02:41,817] [INFO] Running command: blastn -query GCF_003298775.1_ASM329877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg847af0a5-932d-43ac-9b16-96ba12a63055/dqc_reference/reference_markers_gtdb.fasta -out GCF_003298775.1_ASM329877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:43,915] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:43,918] [INFO] Selected 21 target genomes.
[2024-01-25 20:02:43,918] [INFO] Target genome list was writen to GCF_003298775.1_ASM329877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:43,970] [INFO] Task started: fastANI
[2024-01-25 20:02:43,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f5c997-357b-4596-88d0-60481020db33/GCF_003298775.1_ASM329877v1_genomic.fna.gz --refList GCF_003298775.1_ASM329877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003298775.1_ASM329877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:01,813] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:01,825] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:01,825] [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_003298775.1	s__Rhodosalinus sp003298775	100.0	1266	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003385555.1	s__Rhodosalinus sediminis	85.346	811	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	79.9714	614	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	79.6034	601	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314685.1	s__HLUCCA09 sp001314685	79.4542	562	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.4326	555	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	79.3744	550	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834145.1	s__Roseovarius salinarum	79.2906	555	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710275.1	s__Oceanicola sp008710275	79.0329	487	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	78.9811	531	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	78.9604	583	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_900142935.1	s__Rhodovulum sp900142935	78.9586	549	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789055.1	s__Oceanicola lentulus	78.8951	520	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842835.1	s__PHEG01 sp002842835	78.8434	293	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PHEG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	78.5987	480	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278295.1	s__Roseovarius sp016278295	78.5527	401	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116585.1	s__Albibacillus kandeliae	78.473	541	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003605175.1	s__IMCC34051 sp003605175	78.4543	470	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	78.3282	530	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCA_003551745.1	s__Rhodobaculum sp003551745	78.2967	328	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600335.2	s__Rubellimicrobium mesophilum	78.0572	415	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:01,827] [INFO] GTDB search result was written to GCF_003298775.1_ASM329877v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:01,827] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:01,831] [INFO] DFAST_QC result json was written to GCF_003298775.1_ASM329877v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:01,831] [INFO] DFAST_QC completed!
[2024-01-25 20:03:01,831] [INFO] Total running time: 0h1m41s