[2024-01-24 10:47:06,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,593] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bfd7a3b-66be-440a-aab6-d8fdaed35f14/dqc_reference
[2024-01-24 10:47:12,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,810] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,811] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bc97bdd-6c4b-4a73-a7ca-02741ed31d2c/GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/cds.fna -a GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:27,310] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:27,310] [INFO] Task started: HMMsearch
[2024-01-24 10:47:27,310] [INFO] Running command: hmmsearch --tblout GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bfd7a3b-66be-440a-aab6-d8fdaed35f14/dqc_reference/reference_markers.hmm GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:27,637] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:27,638] [INFO] Found 6/6 markers.
[2024-01-24 10:47:27,682] [INFO] Query marker FASTA was written to GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 10:47:27,683] [INFO] Task started: Blastn
[2024-01-24 10:47:27,683] [INFO] Running command: blastn -query GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bfd7a3b-66be-440a-aab6-d8fdaed35f14/dqc_reference/reference_markers.fasta -out GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:28,880] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:28,885] [INFO] Selected 23 target genomes.
[2024-01-24 10:47:28,885] [INFO] Target genome list was writen to GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 10:47:30,150] [INFO] Task started: fastANI
[2024-01-24 10:47:30,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bc97bdd-6c4b-4a73-a7ca-02741ed31d2c/GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna.gz --refList GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:54,680] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:54,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bfd7a3b-66be-440a-aab6-d8fdaed35f14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:54,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bfd7a3b-66be-440a-aab6-d8fdaed35f14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:54,699] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:54,699] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:54,700] [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
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	100.0	1682	1684	95	conclusive
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	78.2817	531	1684	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	78.1719	480	1684	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	77.9036	468	1684	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	77.8225	394	1684	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	77.8068	390	1684	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	77.8037	381	1684	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	77.7052	436	1684	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	77.6502	374	1684	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.6046	417	1684	95	below_threshold
Propylenella binzhouense	strain=L72	GCA_009866965.1	2555902	2555902	type	True	77.5214	324	1684	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	77.5103	422	1684	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	77.4873	369	1684	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.4685	286	1684	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.4632	288	1684	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	77.4421	359	1684	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	77.426	315	1684	95	below_threshold
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	77.4248	292	1684	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.4067	324	1684	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.2204	347	1684	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	77.1668	400	1684	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	77.1571	338	1684	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.9388	366	1684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:54,701] [INFO] DFAST Taxonomy check result was written to GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 10:47:54,703] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:54,703] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:54,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bfd7a3b-66be-440a-aab6-d8fdaed35f14/dqc_reference/checkm_data
[2024-01-24 10:47:54,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:54,757] [INFO] Task started: CheckM
[2024-01-24 10:47:54,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/checkm_input GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 10:48:38,676] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:38,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:38,735] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:38,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:38,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 10:48:38,737] [INFO] Task started: Blastn
[2024-01-24 10:48:38,737] [INFO] Running command: blastn -query GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bfd7a3b-66be-440a-aab6-d8fdaed35f14/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:41,145] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:41,150] [INFO] Selected 15 target genomes.
[2024-01-24 10:48:41,150] [INFO] Target genome list was writen to GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:41,195] [INFO] Task started: fastANI
[2024-01-24 10:48:41,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bc97bdd-6c4b-4a73-a7ca-02741ed31d2c/GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna.gz --refList GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:53,831] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:53,846] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:53,847] [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_900104485.1	s__Bauldia litoralis	100.0	1682	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Bauldia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017305635.1	s__Bauldia sp017305635	78.9517	610	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Bauldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	78.2595	536	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	78.1963	508	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307955.1	s__Kaistia sp017307955	78.0576	509	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	77.9809	539	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258835.1	s__Rhodobium orientis	77.808	381	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCF_015904235.1	s__L22 sp015904235	77.7039	438	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966715.1	s__Blastochloris tepida	77.3725	323	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148505.1	s__Pseudoxanthobacter soli	77.307	358	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526635.1	s__Aquamicrobium_A sp000526635	77.2879	254	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	99.33	98.68	0.94	0.89	3	-
GCF_015482775.1	s__Kaustia mangrovi	77.2399	278	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Kaustia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716745.1	s__GCA-013693735 sp016716745	77.1391	327	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693835.1	s__Rubrimonas sp007693835	76.1891	190	1684	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:53,850] [INFO] GTDB search result was written to GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:53,850] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:53,856] [INFO] DFAST_QC result json was written to GCF_900104485.1_IMG-taxon_2597490370_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 10:48:53,856] [INFO] DFAST_QC completed!
[2024-01-24 10:48:53,856] [INFO] Total running time: 0h1m47s