[2024-01-24 15:09:55,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:09:55,954] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:09:55,954] [INFO] DQC Reference Directory: /var/lib/cwl/stg537527ef-05a4-48a0-ad8c-c2c1f017597e/dqc_reference
[2024-01-24 15:09:58,168] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:09:58,173] [INFO] Task started: Prodigal
[2024-01-24 15:09:58,173] [INFO] Running command: gunzip -c /var/lib/cwl/stg065a51ed-d27b-468e-a261-0ec439fb29c7/GCF_010894475.1_ASM1089447v1_genomic.fna.gz | prodigal -d GCF_010894475.1_ASM1089447v1_genomic.fna/cds.fna -a GCF_010894475.1_ASM1089447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:30,801] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:30,801] [INFO] Task started: HMMsearch
[2024-01-24 15:10:30,802] [INFO] Running command: hmmsearch --tblout GCF_010894475.1_ASM1089447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg537527ef-05a4-48a0-ad8c-c2c1f017597e/dqc_reference/reference_markers.hmm GCF_010894475.1_ASM1089447v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:31,317] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:31,318] [INFO] Found 6/6 markers.
[2024-01-24 15:10:31,389] [INFO] Query marker FASTA was written to GCF_010894475.1_ASM1089447v1_genomic.fna/markers.fasta
[2024-01-24 15:10:31,389] [INFO] Task started: Blastn
[2024-01-24 15:10:31,389] [INFO] Running command: blastn -query GCF_010894475.1_ASM1089447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg537527ef-05a4-48a0-ad8c-c2c1f017597e/dqc_reference/reference_markers.fasta -out GCF_010894475.1_ASM1089447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:32,133] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:32,137] [INFO] Selected 16 target genomes.
[2024-01-24 15:10:32,138] [INFO] Target genome list was writen to GCF_010894475.1_ASM1089447v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:32,146] [INFO] Task started: fastANI
[2024-01-24 15:10:32,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg065a51ed-d27b-468e-a261-0ec439fb29c7/GCF_010894475.1_ASM1089447v1_genomic.fna.gz --refList GCF_010894475.1_ASM1089447v1_genomic.fna/target_genomes.txt --output GCF_010894475.1_ASM1089447v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:03,208] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:03,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg537527ef-05a4-48a0-ad8c-c2c1f017597e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:03,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg537527ef-05a4-48a0-ad8c-c2c1f017597e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:03,228] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:03,228] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:03,228] [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
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	100.0	2490	2534	95	conclusive
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	93.7477	2136	2534	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	93.6612	2165	2534	95	below_threshold
Myxococcus xanthus	strain=DSM 16526	GCA_900106535.1	34	34	type	True	93.6084	2161	2534	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	84.9466	1909	2534	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	84.9106	1896	2534	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	84.7823	1819	2534	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	83.7664	1763	2534	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	82.4197	1556	2534	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	82.2046	1504	2534	95	below_threshold
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	75.1505	119	2534	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	75.1199	85	2534	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.0172	364	2534	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	74.974	178	2534	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.9707	356	2534	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	74.8451	92	2534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:03,230] [INFO] DFAST Taxonomy check result was written to GCF_010894475.1_ASM1089447v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:03,231] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:03,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:03,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg537527ef-05a4-48a0-ad8c-c2c1f017597e/dqc_reference/checkm_data
[2024-01-24 15:11:03,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:03,330] [INFO] Task started: CheckM
[2024-01-24 15:11:03,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010894475.1_ASM1089447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010894475.1_ASM1089447v1_genomic.fna/checkm_input GCF_010894475.1_ASM1089447v1_genomic.fna/checkm_result
[2024-01-24 15:12:59,530] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:59,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:59,561] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:59,561] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:59,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010894475.1_ASM1089447v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:59,562] [INFO] Task started: Blastn
[2024-01-24 15:12:59,562] [INFO] Running command: blastn -query GCF_010894475.1_ASM1089447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg537527ef-05a4-48a0-ad8c-c2c1f017597e/dqc_reference/reference_markers_gtdb.fasta -out GCF_010894475.1_ASM1089447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:13:00,774] [INFO] Task succeeded: Blastn
[2024-01-24 15:13:00,778] [INFO] Selected 9 target genomes.
[2024-01-24 15:13:00,778] [INFO] Target genome list was writen to GCF_010894475.1_ASM1089447v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:13:00,786] [INFO] Task started: fastANI
[2024-01-24 15:13:00,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg065a51ed-d27b-468e-a261-0ec439fb29c7/GCF_010894475.1_ASM1089447v1_genomic.fna.gz --refList GCF_010894475.1_ASM1089447v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010894475.1_ASM1089447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:22,190] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:22,204] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:22,204] [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_013372585.1	s__Myxococcus sp013372585	96.7005	2291	2534	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	99.53	99.53	0.97	0.97	2	conclusive
GCF_006402735.1	s__Myxococcus xanthus_A	94.1082	2184	2534	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.2302	99.44	99.22	0.98	0.96	5	-
GCF_010998615.1	s__Myxococcus sp010998615	93.7749	2119	2534	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.6778	99.99	99.99	0.99	0.99	9	-
GCF_900101905.1	s__Myxococcus virescens	93.6436	2167	2534	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.8216	98.11	97.12	0.95	0.93	4	-
GCF_900106535.1	s__Myxococcus xanthus	93.6005	2162	2534	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.8216	99.36	96.84	0.98	0.91	10	-
GCF_013116825.1	s__Myxococcus xanthus_B	93.488	2097	2534	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	96.6332	99.98	99.98	0.98	0.98	2	-
GCF_002305895.1	s__Myxococcus macrosporus	91.6689	2218	2534	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	98.54	98.54	0.93	0.93	2	-
GCF_014656495.1	s__Myxococcus sp014656495	89.105	2096	2534	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000280925.3	s__Myxococcus hansupus	88.7406	2117	2534	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:13:22,206] [INFO] GTDB search result was written to GCF_010894475.1_ASM1089447v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:22,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:22,213] [INFO] DFAST_QC result json was written to GCF_010894475.1_ASM1089447v1_genomic.fna/dqc_result.json
[2024-01-24 15:13:22,213] [INFO] DFAST_QC completed!
[2024-01-24 15:13:22,213] [INFO] Total running time: 0h3m26s