[2024-01-25 19:07:35,790] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:35,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:35,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c4ac9db-4b18-4462-8681-ed209826decd/dqc_reference
[2024-01-25 19:07:36,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:36,943] [INFO] Task started: Prodigal
[2024-01-25 19:07:36,944] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfd070af-6e44-40a4-be80-716820d09fad/GCF_000224005.2_ASM22400v3_genomic.fna.gz | prodigal -d GCF_000224005.2_ASM22400v3_genomic.fna/cds.fna -a GCF_000224005.2_ASM22400v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:46,554] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:46,555] [INFO] Task started: HMMsearch
[2024-01-25 19:07:46,555] [INFO] Running command: hmmsearch --tblout GCF_000224005.2_ASM22400v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c4ac9db-4b18-4462-8681-ed209826decd/dqc_reference/reference_markers.hmm GCF_000224005.2_ASM22400v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:46,785] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:46,786] [INFO] Found 6/6 markers.
[2024-01-25 19:07:46,816] [INFO] Query marker FASTA was written to GCF_000224005.2_ASM22400v3_genomic.fna/markers.fasta
[2024-01-25 19:07:46,816] [INFO] Task started: Blastn
[2024-01-25 19:07:46,817] [INFO] Running command: blastn -query GCF_000224005.2_ASM22400v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c4ac9db-4b18-4462-8681-ed209826decd/dqc_reference/reference_markers.fasta -out GCF_000224005.2_ASM22400v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:47,663] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:47,665] [INFO] Selected 14 target genomes.
[2024-01-25 19:07:47,666] [INFO] Target genome list was writen to GCF_000224005.2_ASM22400v3_genomic.fna/target_genomes.txt
[2024-01-25 19:07:47,672] [INFO] Task started: fastANI
[2024-01-25 19:07:47,672] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfd070af-6e44-40a4-be80-716820d09fad/GCF_000224005.2_ASM22400v3_genomic.fna.gz --refList GCF_000224005.2_ASM22400v3_genomic.fna/target_genomes.txt --output GCF_000224005.2_ASM22400v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:01,542] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:01,543] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c4ac9db-4b18-4462-8681-ed209826decd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:01,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c4ac9db-4b18-4462-8681-ed209826decd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:01,552] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:08:01,552] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:08:01,552] [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
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	100.0	1259	1259	95	conclusive
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	94.9313	1108	1259	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	94.9258	1142	1259	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	90.8055	1048	1259	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	80.2983	551	1259	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	80.2899	558	1259	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	80.1277	591	1259	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	79.1493	528	1259	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	78.8932	490	1259	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	78.7663	429	1259	95	below_threshold
Thiorhodococcus mannitoliphagus	strain=DSM 18266	GCA_010915725.1	329406	329406	type	True	78.4769	429	1259	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.1556	275	1259	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.6232	238	1259	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.4714	258	1259	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:01,554] [INFO] DFAST Taxonomy check result was written to GCF_000224005.2_ASM22400v3_genomic.fna/tc_result.tsv
[2024-01-25 19:08:01,554] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:01,554] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:01,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c4ac9db-4b18-4462-8681-ed209826decd/dqc_reference/checkm_data
[2024-01-25 19:08:01,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:01,595] [INFO] Task started: CheckM
[2024-01-25 19:08:01,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000224005.2_ASM22400v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000224005.2_ASM22400v3_genomic.fna/checkm_input GCF_000224005.2_ASM22400v3_genomic.fna/checkm_result
[2024-01-25 19:08:44,899] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:44,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:44,915] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:44,915] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:44,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000224005.2_ASM22400v3_genomic.fna/markers.fasta)
[2024-01-25 19:08:44,916] [INFO] Task started: Blastn
[2024-01-25 19:08:44,916] [INFO] Running command: blastn -query GCF_000224005.2_ASM22400v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c4ac9db-4b18-4462-8681-ed209826decd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000224005.2_ASM22400v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:46,495] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:46,498] [INFO] Selected 16 target genomes.
[2024-01-25 19:08:46,499] [INFO] Target genome list was writen to GCF_000224005.2_ASM22400v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:46,511] [INFO] Task started: fastANI
[2024-01-25 19:08:46,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfd070af-6e44-40a4-be80-716820d09fad/GCF_000224005.2_ASM22400v3_genomic.fna.gz --refList GCF_000224005.2_ASM22400v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000224005.2_ASM22400v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:03,667] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:03,676] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:03,677] [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_000224005.2	s__Marichromatium purpuratum	100.0	1259	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004343155.1	s__Marichromatium gracile	94.9258	1142	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_012276755.1	s__Marichromatium bheemlicum	90.8055	1048	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	80.3075	554	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_000585215.1	s__Imhoffiella purpurea	80.2992	579	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018409545.1	s__Allochromatium tepidum	80.2698	559	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013385175.1	s__Allochromatium humboldtianum	80.1744	586	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010820565.1	s__Thiorhodococcus minor	79.1635	526	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583565.1	s__Thiorhodococcus violacea_A	79.123	537	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634315.1	s__Thiocapsa rosea	78.92	489	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399035.1	s__Thiocapsa sp018399035	78.8132	497	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	99.92	99.89	0.99	0.99	3	-
GCF_001499735.1	s__Thiocapsa sp001499735	78.7793	482	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000223985.1	s__Thiocapsa marina	78.7664	468	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390875.1	s__Thiocapsa sp011390875	78.6738	386	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010915725.1	s__Thiorhodococcus mannitoliphagus	78.462	430	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903946935.1	s__Thiodictyon sp903946935	77.7641	401	1259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiodictyon	95.0	99.93	99.89	0.97	0.96	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:03,678] [INFO] GTDB search result was written to GCF_000224005.2_ASM22400v3_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:03,678] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:03,681] [INFO] DFAST_QC result json was written to GCF_000224005.2_ASM22400v3_genomic.fna/dqc_result.json
[2024-01-25 19:09:03,681] [INFO] DFAST_QC completed!
[2024-01-25 19:09:03,682] [INFO] Total running time: 0h1m28s