[2023-06-18 23:43:11,603] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:43:11,625] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:43:11,626] [INFO] DQC Reference Directory: /var/lib/cwl/stga885c78b-c7f3-42b9-aa48-191a08a8341f/dqc_reference
[2023-06-18 23:43:14,149] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:43:14,150] [INFO] Task started: Prodigal
[2023-06-18 23:43:14,151] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cd3ee6c-804d-4265-b46c-1440b3ea5d39/GCA_018780585.1_ASM1878058v1_genomic.fna.gz | prodigal -d GCA_018780585.1_ASM1878058v1_genomic.fna/cds.fna -a GCA_018780585.1_ASM1878058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:43:27,680] [INFO] Task succeeded: Prodigal
[2023-06-18 23:43:27,681] [INFO] Task started: HMMsearch
[2023-06-18 23:43:27,681] [INFO] Running command: hmmsearch --tblout GCA_018780585.1_ASM1878058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga885c78b-c7f3-42b9-aa48-191a08a8341f/dqc_reference/reference_markers.hmm GCA_018780585.1_ASM1878058v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:43:27,976] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:43:27,978] [INFO] Found 6/6 markers.
[2023-06-18 23:43:28,030] [INFO] Query marker FASTA was written to GCA_018780585.1_ASM1878058v1_genomic.fna/markers.fasta
[2023-06-18 23:43:28,030] [INFO] Task started: Blastn
[2023-06-18 23:43:28,030] [INFO] Running command: blastn -query GCA_018780585.1_ASM1878058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga885c78b-c7f3-42b9-aa48-191a08a8341f/dqc_reference/reference_markers.fasta -out GCA_018780585.1_ASM1878058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:43:28,892] [INFO] Task succeeded: Blastn
[2023-06-18 23:43:28,901] [INFO] Selected 22 target genomes.
[2023-06-18 23:43:28,901] [INFO] Target genome list was writen to GCA_018780585.1_ASM1878058v1_genomic.fna/target_genomes.txt
[2023-06-18 23:43:28,912] [INFO] Task started: fastANI
[2023-06-18 23:43:28,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cd3ee6c-804d-4265-b46c-1440b3ea5d39/GCA_018780585.1_ASM1878058v1_genomic.fna.gz --refList GCA_018780585.1_ASM1878058v1_genomic.fna/target_genomes.txt --output GCA_018780585.1_ASM1878058v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:43:47,652] [INFO] Task succeeded: fastANI
[2023-06-18 23:43:47,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga885c78b-c7f3-42b9-aa48-191a08a8341f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:43:47,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga885c78b-c7f3-42b9-aa48-191a08a8341f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:43:47,672] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 23:43:47,672] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 23:43:47,672] [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
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	93.8875	1263	1481	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	87.1451	1116	1481	95	below_threshold
Methyloversatilis thermotolerans	strain=3t	GCA_000372885.1	1346290	1346290	type	True	83.4432	955	1481	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.7757	453	1481	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	78.5387	348	1481	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	78.5029	358	1481	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	78.4848	378	1481	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.476	405	1481	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	78.4433	418	1481	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	78.4188	435	1481	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	78.2696	474	1481	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	78.2434	473	1481	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.1364	387	1481	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.5544	239	1481	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	77.3747	243	1481	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	76.2995	258	1481	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	75.9573	143	1481	95	below_threshold
Mesorhizobium albiziae	strain=DSM 21822	GCA_900114255.1	335020	335020	type	True	75.5695	116	1481	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.5148	208	1481	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	75.3892	111	1481	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	75.3324	147	1481	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	75.3315	141	1481	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 23:43:47,675] [INFO] DFAST Taxonomy check result was written to GCA_018780585.1_ASM1878058v1_genomic.fna/tc_result.tsv
[2023-06-18 23:43:47,675] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:43:47,675] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:43:47,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga885c78b-c7f3-42b9-aa48-191a08a8341f/dqc_reference/checkm_data
[2023-06-18 23:43:47,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:43:47,720] [INFO] Task started: CheckM
[2023-06-18 23:43:47,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018780585.1_ASM1878058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018780585.1_ASM1878058v1_genomic.fna/checkm_input GCA_018780585.1_ASM1878058v1_genomic.fna/checkm_result
[2023-06-18 23:44:34,153] [INFO] Task succeeded: CheckM
[2023-06-18 23:44:34,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 23:44:34,174] [INFO] ===== Completeness check finished =====
[2023-06-18 23:44:34,174] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:44:34,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018780585.1_ASM1878058v1_genomic.fna/markers.fasta)
[2023-06-18 23:44:34,175] [INFO] Task started: Blastn
[2023-06-18 23:44:34,175] [INFO] Running command: blastn -query GCA_018780585.1_ASM1878058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga885c78b-c7f3-42b9-aa48-191a08a8341f/dqc_reference/reference_markers_gtdb.fasta -out GCA_018780585.1_ASM1878058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:44:35,637] [INFO] Task succeeded: Blastn
[2023-06-18 23:44:35,643] [INFO] Selected 12 target genomes.
[2023-06-18 23:44:35,643] [INFO] Target genome list was writen to GCA_018780585.1_ASM1878058v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:44:35,652] [INFO] Task started: fastANI
[2023-06-18 23:44:35,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cd3ee6c-804d-4265-b46c-1440b3ea5d39/GCA_018780585.1_ASM1878058v1_genomic.fna.gz --refList GCA_018780585.1_ASM1878058v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018780585.1_ASM1878058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:44:47,365] [INFO] Task succeeded: fastANI
[2023-06-18 23:44:47,380] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 23:44:47,380] [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_000385375.1	s__Methyloversatilis discipulorum_A	95.096	1267	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	95.78	95.10	0.90	0.89	4	conclusive
GCF_000527135.1	s__Methyloversatilis discipulorum	93.8875	1263	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	97.77	95.54	0.94	0.88	3	-
GCF_000214035.2	s__Methyloversatilis universalis	87.1337	1117	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000378945.1	s__Methyloversatilis universalis_A	86.9106	1073	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791045.1	s__Methyloversatilis sp016791045	83.8397	844	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713355.1	s__Methyloversatilis sp001713355	83.6238	929	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372885.1	s__Methyloversatilis thermotolerans	83.4514	955	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018824085.1	s__Methyloversatilis sp018824085	83.2288	981	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	99.98	99.98	0.99	0.99	4	-
GCA_017302315.1	s__Zoogloea sp017302315	77.4859	274	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114255.1	s__Mesorhizobium_F albiziae	75.5898	116	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425965.1	s__Mesorhizobium sp000425965	75.5299	112	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012971745.1	s__ORNL1 sp012971745	75.4521	166	1481	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__ORNL1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 23:44:47,382] [INFO] GTDB search result was written to GCA_018780585.1_ASM1878058v1_genomic.fna/result_gtdb.tsv
[2023-06-18 23:44:47,383] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:44:47,386] [INFO] DFAST_QC result json was written to GCA_018780585.1_ASM1878058v1_genomic.fna/dqc_result.json
[2023-06-18 23:44:47,387] [INFO] DFAST_QC completed!
[2023-06-18 23:44:47,387] [INFO] Total running time: 0h1m36s