[2024-01-24 14:10:15,992] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:10:15,994] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:10:15,994] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f31647c-037b-466c-8fa7-f5e757529428/dqc_reference
[2024-01-24 14:10:17,393] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:10:17,394] [INFO] Task started: Prodigal
[2024-01-24 14:10:17,394] [INFO] Running command: gunzip -c /var/lib/cwl/stg0498d027-fb7f-41a3-b9f0-d447b406040b/GCF_019203965.1_ASM1920396v1_genomic.fna.gz | prodigal -d GCF_019203965.1_ASM1920396v1_genomic.fna/cds.fna -a GCF_019203965.1_ASM1920396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:10:27,467] [INFO] Task succeeded: Prodigal
[2024-01-24 14:10:27,467] [INFO] Task started: HMMsearch
[2024-01-24 14:10:27,468] [INFO] Running command: hmmsearch --tblout GCF_019203965.1_ASM1920396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f31647c-037b-466c-8fa7-f5e757529428/dqc_reference/reference_markers.hmm GCF_019203965.1_ASM1920396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:10:27,754] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:10:27,755] [INFO] Found 6/6 markers.
[2024-01-24 14:10:27,786] [INFO] Query marker FASTA was written to GCF_019203965.1_ASM1920396v1_genomic.fna/markers.fasta
[2024-01-24 14:10:27,786] [INFO] Task started: Blastn
[2024-01-24 14:10:27,787] [INFO] Running command: blastn -query GCF_019203965.1_ASM1920396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f31647c-037b-466c-8fa7-f5e757529428/dqc_reference/reference_markers.fasta -out GCF_019203965.1_ASM1920396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:28,690] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:28,694] [INFO] Selected 16 target genomes.
[2024-01-24 14:10:28,695] [INFO] Target genome list was writen to GCF_019203965.1_ASM1920396v1_genomic.fna/target_genomes.txt
[2024-01-24 14:10:28,703] [INFO] Task started: fastANI
[2024-01-24 14:10:28,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg0498d027-fb7f-41a3-b9f0-d447b406040b/GCF_019203965.1_ASM1920396v1_genomic.fna.gz --refList GCF_019203965.1_ASM1920396v1_genomic.fna/target_genomes.txt --output GCF_019203965.1_ASM1920396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:10:43,464] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:43,465] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f31647c-037b-466c-8fa7-f5e757529428/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:10:43,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f31647c-037b-466c-8fa7-f5e757529428/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:10:43,486] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:10:43,486] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:10:43,486] [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
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	100.0	1121	1122	95	conclusive
Elioraea rosea	strain=PF-30	GCA_007644105.1	2492390	2492390	type	True	81.908	781	1122	95	below_threshold
Elioraea thermophila	strain=YIM 72297	GCA_003336755.1	2185104	2185104	type	True	79.4567	554	1122	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.9588	479	1122	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.6444	338	1122	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	77.5345	194	1122	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	77.4295	346	1122	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	77.4099	339	1122	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.208	324	1122	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	77.136	264	1122	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.9147	303	1122	95	below_threshold
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	76.9127	347	1122	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	76.85	357	1122	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.5117	259	1122	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.3425	199	1122	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	76.3241	204	1122	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:10:43,488] [INFO] DFAST Taxonomy check result was written to GCF_019203965.1_ASM1920396v1_genomic.fna/tc_result.tsv
[2024-01-24 14:10:43,488] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:10:43,489] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:10:43,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f31647c-037b-466c-8fa7-f5e757529428/dqc_reference/checkm_data
[2024-01-24 14:10:43,490] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:10:43,524] [INFO] Task started: CheckM
[2024-01-24 14:10:43,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019203965.1_ASM1920396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019203965.1_ASM1920396v1_genomic.fna/checkm_input GCF_019203965.1_ASM1920396v1_genomic.fna/checkm_result
[2024-01-24 14:11:20,161] [INFO] Task succeeded: CheckM
[2024-01-24 14:11:20,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:11:20,182] [INFO] ===== Completeness check finished =====
[2024-01-24 14:11:20,182] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:11:20,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019203965.1_ASM1920396v1_genomic.fna/markers.fasta)
[2024-01-24 14:11:20,183] [INFO] Task started: Blastn
[2024-01-24 14:11:20,183] [INFO] Running command: blastn -query GCF_019203965.1_ASM1920396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f31647c-037b-466c-8fa7-f5e757529428/dqc_reference/reference_markers_gtdb.fasta -out GCF_019203965.1_ASM1920396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:11:21,753] [INFO] Task succeeded: Blastn
[2024-01-24 14:11:21,758] [INFO] Selected 12 target genomes.
[2024-01-24 14:11:21,758] [INFO] Target genome list was writen to GCF_019203965.1_ASM1920396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:11:21,788] [INFO] Task started: fastANI
[2024-01-24 14:11:21,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg0498d027-fb7f-41a3-b9f0-d447b406040b/GCF_019203965.1_ASM1920396v1_genomic.fna.gz --refList GCF_019203965.1_ASM1920396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019203965.1_ASM1920396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:11:31,915] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:31,925] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:11:31,926] [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_019203965.1	s__Elioraea_A sp019203965	100.0	1122	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007644105.1	s__Elioraea_A rosea	81.9113	781	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006704265.1	s__Elioraea sp006704265	80.6249	630	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378465.1	s__Elioraea tepidiphila	80.2076	675	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336755.1	s__Elioraea thermophila	79.4529	554	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Elioraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644455.1	s__Caldovatus sediminis	78.0889	488	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425365.1	s__Roseococcus flocculans	78.0416	429	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761865.1	s__Crenalkalicoccus roseus	77.9632	443	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	77.9588	479	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_000164635.1	s__Roseomonas cervicalis	77.6757	336	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307285.1	s__JAFKFI01 sp017307285	77.2144	250	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015223225.1	s__Roseomonas sp015223225	76.7395	256	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:11:31,927] [INFO] GTDB search result was written to GCF_019203965.1_ASM1920396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:11:31,928] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:11:31,932] [INFO] DFAST_QC result json was written to GCF_019203965.1_ASM1920396v1_genomic.fna/dqc_result.json
[2024-01-24 14:11:31,932] [INFO] DFAST_QC completed!
[2024-01-24 14:11:31,932] [INFO] Total running time: 0h1m16s