[2024-01-24 13:36:30,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:30,923] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:30,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg70281b0b-f835-4774-b2d0-578ebdaec959/dqc_reference
[2024-01-24 13:36:32,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:32,281] [INFO] Task started: Prodigal
[2024-01-24 13:36:32,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg92969cbd-311d-42ba-9f13-8c4b01797c8f/GCF_004358185.1_ASM435818v1_genomic.fna.gz | prodigal -d GCF_004358185.1_ASM435818v1_genomic.fna/cds.fna -a GCF_004358185.1_ASM435818v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:45,600] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:45,600] [INFO] Task started: HMMsearch
[2024-01-24 13:36:45,601] [INFO] Running command: hmmsearch --tblout GCF_004358185.1_ASM435818v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70281b0b-f835-4774-b2d0-578ebdaec959/dqc_reference/reference_markers.hmm GCF_004358185.1_ASM435818v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:45,892] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:45,894] [INFO] Found 6/6 markers.
[2024-01-24 13:36:45,935] [INFO] Query marker FASTA was written to GCF_004358185.1_ASM435818v1_genomic.fna/markers.fasta
[2024-01-24 13:36:45,936] [INFO] Task started: Blastn
[2024-01-24 13:36:45,936] [INFO] Running command: blastn -query GCF_004358185.1_ASM435818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70281b0b-f835-4774-b2d0-578ebdaec959/dqc_reference/reference_markers.fasta -out GCF_004358185.1_ASM435818v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:46,838] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:46,842] [INFO] Selected 18 target genomes.
[2024-01-24 13:36:46,843] [INFO] Target genome list was writen to GCF_004358185.1_ASM435818v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:46,858] [INFO] Task started: fastANI
[2024-01-24 13:36:46,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg92969cbd-311d-42ba-9f13-8c4b01797c8f/GCF_004358185.1_ASM435818v1_genomic.fna.gz --refList GCF_004358185.1_ASM435818v1_genomic.fna/target_genomes.txt --output GCF_004358185.1_ASM435818v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:02,564] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:02,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70281b0b-f835-4774-b2d0-578ebdaec959/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:02,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70281b0b-f835-4774-b2d0-578ebdaec959/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:02,578] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:02,579] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:02,579] [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
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	100.0	1514	1518	95	conclusive
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	84.7059	1005	1518	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	81.9646	811	1518	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	81.9248	825	1518	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	80.9104	769	1518	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	80.8	728	1518	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	80.7975	748	1518	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	80.4548	639	1518	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	80.1571	656	1518	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	79.9231	697	1518	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	79.2223	558	1518	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.0446	504	1518	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.7235	439	1518	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.562	462	1518	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	78.4137	498	1518	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.0473	400	1518	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.907	423	1518	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.7315	191	1518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:02,580] [INFO] DFAST Taxonomy check result was written to GCF_004358185.1_ASM435818v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:02,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:02,581] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:02,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70281b0b-f835-4774-b2d0-578ebdaec959/dqc_reference/checkm_data
[2024-01-24 13:37:02,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:02,629] [INFO] Task started: CheckM
[2024-01-24 13:37:02,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004358185.1_ASM435818v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004358185.1_ASM435818v1_genomic.fna/checkm_input GCF_004358185.1_ASM435818v1_genomic.fna/checkm_result
[2024-01-24 13:37:47,287] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:47,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:47,311] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:47,311] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:47,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004358185.1_ASM435818v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:47,312] [INFO] Task started: Blastn
[2024-01-24 13:37:47,312] [INFO] Running command: blastn -query GCF_004358185.1_ASM435818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70281b0b-f835-4774-b2d0-578ebdaec959/dqc_reference/reference_markers_gtdb.fasta -out GCF_004358185.1_ASM435818v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:48,964] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:48,968] [INFO] Selected 18 target genomes.
[2024-01-24 13:37:48,969] [INFO] Target genome list was writen to GCF_004358185.1_ASM435818v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:48,995] [INFO] Task started: fastANI
[2024-01-24 13:37:48,995] [INFO] Running command: fastANI --query /var/lib/cwl/stg92969cbd-311d-42ba-9f13-8c4b01797c8f/GCF_004358185.1_ASM435818v1_genomic.fna.gz --refList GCF_004358185.1_ASM435818v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004358185.1_ASM435818v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:05,491] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:05,506] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:05,506] [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_004358185.1	s__Antarcticimicrobium luteum	100.0	1514	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004348975.1	s__Antarcticimicrobium sediminis	84.7059	1005	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	81.9694	811	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900109035.1	s__Cribrihabitans marinus	80.796	748	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003511785.1	s__UBA7951 sp003511785	80.7214	495	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	80.7015	696	1518	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_900142185.1	s__Lutimaribacter pacificus	80.4866	727	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900129345.1	s__Ruegeria intermedia	80.4451	640	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	80.3474	686	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	80.2364	674	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	80.0779	768	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	79.9436	695	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	79.4165	432	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434965.1	s__Marimonas lutisalis	79.1937	592	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	79.189	562	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401465.1	s__Aestuariivita sp018401465	78.9277	610	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210165.1	s__CAU-1492 sp002210165	78.7536	555	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016758075.1	s__CAU-1492 sp016758075	78.3835	537	1518	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1492	95.0	99.98	99.98	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:05,508] [INFO] GTDB search result was written to GCF_004358185.1_ASM435818v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:05,509] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:05,516] [INFO] DFAST_QC result json was written to GCF_004358185.1_ASM435818v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:05,516] [INFO] DFAST_QC completed!
[2024-01-24 13:38:05,516] [INFO] Total running time: 0h1m35s