[2023-06-12 23:46:04,177] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:46:04,183] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:46:04,183] [INFO] DQC Reference Directory: /var/lib/cwl/stg447c9839-b7bc-4383-986f-c36a8fcff99d/dqc_reference
[2023-06-12 23:46:05,480] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:46:05,481] [INFO] Task started: Prodigal
[2023-06-12 23:46:05,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg94bd3d83-3407-4457-8287-617f0d66ba14/GCA_022448005.1_ASM2244800v1_genomic.fna.gz | prodigal -d GCA_022448005.1_ASM2244800v1_genomic.fna/cds.fna -a GCA_022448005.1_ASM2244800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:46:19,518] [INFO] Task succeeded: Prodigal
[2023-06-12 23:46:19,519] [INFO] Task started: HMMsearch
[2023-06-12 23:46:19,519] [INFO] Running command: hmmsearch --tblout GCA_022448005.1_ASM2244800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg447c9839-b7bc-4383-986f-c36a8fcff99d/dqc_reference/reference_markers.hmm GCA_022448005.1_ASM2244800v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:46:19,819] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:46:19,821] [INFO] Found 6/6 markers.
[2023-06-12 23:46:19,867] [INFO] Query marker FASTA was written to GCA_022448005.1_ASM2244800v1_genomic.fna/markers.fasta
[2023-06-12 23:46:19,867] [INFO] Task started: Blastn
[2023-06-12 23:46:19,867] [INFO] Running command: blastn -query GCA_022448005.1_ASM2244800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg447c9839-b7bc-4383-986f-c36a8fcff99d/dqc_reference/reference_markers.fasta -out GCA_022448005.1_ASM2244800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:46:20,713] [INFO] Task succeeded: Blastn
[2023-06-12 23:46:20,721] [INFO] Selected 12 target genomes.
[2023-06-12 23:46:20,722] [INFO] Target genome list was writen to GCA_022448005.1_ASM2244800v1_genomic.fna/target_genomes.txt
[2023-06-12 23:46:20,726] [INFO] Task started: fastANI
[2023-06-12 23:46:20,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg94bd3d83-3407-4457-8287-617f0d66ba14/GCA_022448005.1_ASM2244800v1_genomic.fna.gz --refList GCA_022448005.1_ASM2244800v1_genomic.fna/target_genomes.txt --output GCA_022448005.1_ASM2244800v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:46:31,874] [INFO] Task succeeded: fastANI
[2023-06-12 23:46:31,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg447c9839-b7bc-4383-986f-c36a8fcff99d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:46:31,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg447c9839-b7bc-4383-986f-c36a8fcff99d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:46:31,885] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:46:31,885] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 23:46:31,885] [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
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_024328335.1	271420	271420	suspected-type	True	88.4024	1165	1579	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_900129835.1	271420	271420	suspected-type	True	88.3669	1185	1579	95	below_threshold
[Pseudomonas] zhaodongensis	strain=NEAU-ST5-21	GCA_003696365.1	1176257	1176257	suspected-type	True	82.2129	968	1579	95	below_threshold
[Pseudomonas] zhaodongensis	strain=DSM 27559T	GCA_024448735.1	1176257	1176257	suspected-type	True	82.2106	957	1579	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	81.618	843	1579	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	81.2616	817	1579	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	81.1861	745	1579	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	81.1646	812	1579	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	81.1479	753	1579	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	81.1324	743	1579	95	below_threshold
Pseudomonas saudiphocaensis	strain=20_BN	GCA_000756775.2	1499686	1499686	type	True	80.6	709	1579	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	78.728	432	1579	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 23:46:31,887] [INFO] DFAST Taxonomy check result was written to GCA_022448005.1_ASM2244800v1_genomic.fna/tc_result.tsv
[2023-06-12 23:46:31,888] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:46:31,888] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:46:31,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg447c9839-b7bc-4383-986f-c36a8fcff99d/dqc_reference/checkm_data
[2023-06-12 23:46:31,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:46:31,939] [INFO] Task started: CheckM
[2023-06-12 23:46:31,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022448005.1_ASM2244800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022448005.1_ASM2244800v1_genomic.fna/checkm_input GCA_022448005.1_ASM2244800v1_genomic.fna/checkm_result
[2023-06-12 23:47:14,593] [INFO] Task succeeded: CheckM
[2023-06-12 23:47:14,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:47:14,620] [INFO] ===== Completeness check finished =====
[2023-06-12 23:47:14,621] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:47:14,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022448005.1_ASM2244800v1_genomic.fna/markers.fasta)
[2023-06-12 23:47:14,622] [INFO] Task started: Blastn
[2023-06-12 23:47:14,622] [INFO] Running command: blastn -query GCA_022448005.1_ASM2244800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg447c9839-b7bc-4383-986f-c36a8fcff99d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022448005.1_ASM2244800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:47:16,074] [INFO] Task succeeded: Blastn
[2023-06-12 23:47:16,079] [INFO] Selected 12 target genomes.
[2023-06-12 23:47:16,079] [INFO] Target genome list was writen to GCA_022448005.1_ASM2244800v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:47:16,087] [INFO] Task started: fastANI
[2023-06-12 23:47:16,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg94bd3d83-3407-4457-8287-617f0d66ba14/GCA_022448005.1_ASM2244800v1_genomic.fna.gz --refList GCA_022448005.1_ASM2244800v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022448005.1_ASM2244800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:47:29,462] [INFO] Task succeeded: fastANI
[2023-06-12 23:47:29,475] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-12 23:47:29,476] [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_002890895.1	s__Pseudomonas_A stutzeri_AB	94.9227	1259	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.17	97.01	0.91	0.85	18	-
GCA_004010935.1	s__Pseudomonas_A sp004010935	88.5379	1288	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	96.94	95.82	0.92	0.89	15	-
GCF_900129835.1	s__Pseudomonas_A xanthomarina	88.3669	1185	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000235745.1	s__Pseudomonas_A stutzeri_H	87.4194	1062	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339675.1	s__Pseudomonas_A stutzeri_O	83.4611	1052	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002387205.1	s__Pseudomonas_A stutzeri_N	83.3767	1013	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.23	98.23	0.88	0.88	2	-
GCF_018138085.1	s__Pseudomonas_A stutzeri_AI	83.3292	1090	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.15	96.92	0.90	0.86	5	-
GCF_019090095.1	s__Pseudomonas_A stutzeri_AN	83.1365	1047	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003325755.1	s__Pseudomonas_A sp003325755	82.9275	1042	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452485.1	s__Pseudomonas_A stutzeri_P	82.6834	969	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002476945.1	s__Pseudomonas_A stutzeri_Q	82.4075	1024	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696365.1	s__Pseudomonas_A zhaodongensis	82.213	968	1579	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 23:47:29,478] [INFO] GTDB search result was written to GCA_022448005.1_ASM2244800v1_genomic.fna/result_gtdb.tsv
[2023-06-12 23:47:29,479] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:47:29,482] [INFO] DFAST_QC result json was written to GCA_022448005.1_ASM2244800v1_genomic.fna/dqc_result.json
[2023-06-12 23:47:29,482] [INFO] DFAST_QC completed!
[2023-06-12 23:47:29,482] [INFO] Total running time: 0h1m25s