[2024-01-25 18:48:35,605] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:35,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:35,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg54b20425-0f95-4a6a-abc2-50726d9462ea/dqc_reference
[2024-01-25 18:48:36,821] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:36,822] [INFO] Task started: Prodigal
[2024-01-25 18:48:36,822] [INFO] Running command: gunzip -c /var/lib/cwl/stg3499bc4a-a7b5-4374-801b-8e75593990a5/GCF_025273675.1_ASM2527367v1_genomic.fna.gz | prodigal -d GCF_025273675.1_ASM2527367v1_genomic.fna/cds.fna -a GCF_025273675.1_ASM2527367v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:24,268] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:24,269] [INFO] Task started: HMMsearch
[2024-01-25 18:49:24,269] [INFO] Running command: hmmsearch --tblout GCF_025273675.1_ASM2527367v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54b20425-0f95-4a6a-abc2-50726d9462ea/dqc_reference/reference_markers.hmm GCF_025273675.1_ASM2527367v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:24,528] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:24,529] [INFO] Found 6/6 markers.
[2024-01-25 18:49:24,578] [INFO] Query marker FASTA was written to GCF_025273675.1_ASM2527367v1_genomic.fna/markers.fasta
[2024-01-25 18:49:24,578] [INFO] Task started: Blastn
[2024-01-25 18:49:24,578] [INFO] Running command: blastn -query GCF_025273675.1_ASM2527367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54b20425-0f95-4a6a-abc2-50726d9462ea/dqc_reference/reference_markers.fasta -out GCF_025273675.1_ASM2527367v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:25,703] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:25,706] [INFO] Selected 18 target genomes.
[2024-01-25 18:49:25,706] [INFO] Target genome list was writen to GCF_025273675.1_ASM2527367v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:25,724] [INFO] Task started: fastANI
[2024-01-25 18:49:25,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg3499bc4a-a7b5-4374-801b-8e75593990a5/GCF_025273675.1_ASM2527367v1_genomic.fna.gz --refList GCF_025273675.1_ASM2527367v1_genomic.fna/target_genomes.txt --output GCF_025273675.1_ASM2527367v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:44,155] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:44,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54b20425-0f95-4a6a-abc2-50726d9462ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:44,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54b20425-0f95-4a6a-abc2-50726d9462ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:44,167] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:49:44,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:44,167] [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
Gordonia pseudamarae	strain=CON9	GCA_025273675.1	2831662	2831662	type	True	100.0	1713	1715	95	conclusive
Gordonia amarae	strain=NBRC 15530	GCA_000241345.2	36821	36821	type	True	85.0588	1210	1715	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	79.4309	660	1715	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	79.4203	662	1715	95	below_threshold
Gordonia alkanivorans	strain=NBRC 16433	GCA_000225505.1	84096	84096	type	True	79.3848	658	1715	95	below_threshold
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	79.3657	699	1715	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	79.3639	662	1715	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_024734075.1	2665643	2665643	type	True	79.1675	657	1715	95	below_threshold
Gordonia rhizosphera	strain=NBRC 16068	GCA_000298195.1	83341	83341	type	True	79.1284	633	1715	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_009828195.1	2665643	2665643	type	True	79.0087	648	1715	95	below_threshold
Gordonia terrae	strain=3612	GCA_001698225.1	2055	2055	suspected-type	True	78.9708	661	1715	95	below_threshold
Gordonia terrae	strain=NRRL B-16283	GCA_003183825.1	2055	2055	suspected-type	True	78.9291	680	1715	95	below_threshold
Gordonia terrae	strain=NBRC 100016	GCA_000248035.2	2055	2055	suspected-type	True	78.8786	647	1715	95	below_threshold
Gordonia sputi	strain=ATCC 29627	GCA_012396255.1	36823	36823	type	True	78.6633	520	1715	95	below_threshold
Gordonia sputi	strain=NBRC 100414	GCA_000248055.2	36823	36823	type	True	78.6358	513	1715	95	below_threshold
Gordonia asplenii	strain=TBRC 11910	GCA_012933505.1	2725283	2725283	type	True	78.581	587	1715	95	below_threshold
Gordonia araii	strain=NBRC 100433	GCA_000241265.2	263909	263909	type	True	78.5503	471	1715	95	below_threshold
Gordonia araii	strain=IFM 10211	GCA_013004535.1	263909	263909	type	True	78.5382	471	1715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:44,168] [INFO] DFAST Taxonomy check result was written to GCF_025273675.1_ASM2527367v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:44,169] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:44,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:44,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54b20425-0f95-4a6a-abc2-50726d9462ea/dqc_reference/checkm_data
[2024-01-25 18:49:44,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:44,218] [INFO] Task started: CheckM
[2024-01-25 18:49:44,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025273675.1_ASM2527367v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025273675.1_ASM2527367v1_genomic.fna/checkm_input GCF_025273675.1_ASM2527367v1_genomic.fna/checkm_result
[2024-01-25 18:52:08,787] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:08,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:08,821] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:08,822] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:08,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025273675.1_ASM2527367v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:08,827] [INFO] Task started: Blastn
[2024-01-25 18:52:08,827] [INFO] Running command: blastn -query GCF_025273675.1_ASM2527367v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54b20425-0f95-4a6a-abc2-50726d9462ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_025273675.1_ASM2527367v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:10,566] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:10,571] [INFO] Selected 17 target genomes.
[2024-01-25 18:52:10,571] [INFO] Target genome list was writen to GCF_025273675.1_ASM2527367v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:10,609] [INFO] Task started: fastANI
[2024-01-25 18:52:10,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg3499bc4a-a7b5-4374-801b-8e75593990a5/GCF_025273675.1_ASM2527367v1_genomic.fna.gz --refList GCF_025273675.1_ASM2527367v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025273675.1_ASM2527367v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:28,863] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:28,874] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:28,874] [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_009914535.1	s__Gordonia pseudoamarae	99.9419	1699	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.95	99.95	1.00	1.00	2	conclusive
GCF_000241345.1	s__Gordonia amarae	85.0704	1208	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.98	99.98	0.99	0.99	3	-
GCF_000344155.1	s__Gordonia paraffinivorans	79.6042	644	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.97	98.74	0.93	0.90	12	-
GCF_000327325.1	s__Gordonia rubripertincta	79.4358	659	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_000298235.1	s__Gordonia namibiensis	79.4318	660	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_000225505.1	s__Gordonia alkanivorans	79.4179	654	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
GCF_900105725.1	s__Gordonia westfalica	79.3654	698	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290605.1	s__Gordonia sp002009645	79.2047	630	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
GCA_004193205.1	s__Gordonia sediminis	78.9978	679	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828195.1	s__Gordonia sp009828195	78.9967	652	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797825.1	s__Gordonia sp003797825	78.962	628	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698225.1	s__Gordonia terrae	78.953	662	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	97.67	0.96	0.87	7	-
GCF_002149015.1	s__Gordonia lacunae	78.9284	645	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009862785.1	s__Gordonia sp009862785	78.7111	568	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013348785.1	s__Gordonia sp013348785	78.6733	476	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000248055.1	s__Gordonia sputi	78.6433	512	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.92	96.52	0.90	0.84	5	-
GCF_000241265.1	s__Gordonia araii	78.5332	472	1715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:28,877] [INFO] GTDB search result was written to GCF_025273675.1_ASM2527367v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:28,877] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:28,880] [INFO] DFAST_QC result json was written to GCF_025273675.1_ASM2527367v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:28,880] [INFO] DFAST_QC completed!
[2024-01-25 18:52:28,881] [INFO] Total running time: 0h3m53s