[2024-01-24 13:01:26,241] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,246] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e4988de-4b0e-440d-9a1c-8d6f9f8c9f12/dqc_reference
[2024-01-24 13:01:27,444] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:27,445] [INFO] Task started: Prodigal
[2024-01-24 13:01:27,445] [INFO] Running command: gunzip -c /var/lib/cwl/stgd74e3302-d1a1-4247-937b-0d746501eb35/GCF_000327045.1_ASM32704v1_genomic.fna.gz | prodigal -d GCF_000327045.1_ASM32704v1_genomic.fna/cds.fna -a GCF_000327045.1_ASM32704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:39,636] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:39,637] [INFO] Task started: HMMsearch
[2024-01-24 13:01:39,637] [INFO] Running command: hmmsearch --tblout GCF_000327045.1_ASM32704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e4988de-4b0e-440d-9a1c-8d6f9f8c9f12/dqc_reference/reference_markers.hmm GCF_000327045.1_ASM32704v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:39,932] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:39,934] [INFO] Found 6/6 markers.
[2024-01-24 13:01:39,970] [INFO] Query marker FASTA was written to GCF_000327045.1_ASM32704v1_genomic.fna/markers.fasta
[2024-01-24 13:01:39,970] [INFO] Task started: Blastn
[2024-01-24 13:01:39,970] [INFO] Running command: blastn -query GCF_000327045.1_ASM32704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e4988de-4b0e-440d-9a1c-8d6f9f8c9f12/dqc_reference/reference_markers.fasta -out GCF_000327045.1_ASM32704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:40,986] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:40,990] [INFO] Selected 19 target genomes.
[2024-01-24 13:01:40,991] [INFO] Target genome list was writen to GCF_000327045.1_ASM32704v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:40,999] [INFO] Task started: fastANI
[2024-01-24 13:01:41,000] [INFO] Running command: fastANI --query /var/lib/cwl/stgd74e3302-d1a1-4247-937b-0d746501eb35/GCF_000327045.1_ASM32704v1_genomic.fna.gz --refList GCF_000327045.1_ASM32704v1_genomic.fna/target_genomes.txt --output GCF_000327045.1_ASM32704v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:58,031] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:58,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e4988de-4b0e-440d-9a1c-8d6f9f8c9f12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:58,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e4988de-4b0e-440d-9a1c-8d6f9f8c9f12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:58,046] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:58,046] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:58,047] [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
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	100.0	1378	1378	95	conclusive
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	79.1146	395	1378	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	78.8978	421	1378	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	78.8184	428	1378	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	78.6095	359	1378	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	78.5108	335	1378	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	78.351	368	1378	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	78.3037	379	1378	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	78.3014	336	1378	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	78.1846	354	1378	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	78.179	349	1378	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	77.8284	352	1378	95	below_threshold
Thiocapsa marina	strain=5811	GCA_000223985.2	244573	244573	type	True	77.753	346	1378	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	77.7097	348	1378	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.6938	176	1378	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	76.6753	146	1378	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.562	159	1378	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	76.5432	144	1378	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.4443	159	1378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:58,049] [INFO] DFAST Taxonomy check result was written to GCF_000327045.1_ASM32704v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:58,050] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:58,050] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:58,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e4988de-4b0e-440d-9a1c-8d6f9f8c9f12/dqc_reference/checkm_data
[2024-01-24 13:01:58,051] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:58,098] [INFO] Task started: CheckM
[2024-01-24 13:01:58,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000327045.1_ASM32704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000327045.1_ASM32704v1_genomic.fna/checkm_input GCF_000327045.1_ASM32704v1_genomic.fna/checkm_result
[2024-01-24 13:02:34,681] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:34,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:34,705] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:34,706] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:34,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000327045.1_ASM32704v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:34,707] [INFO] Task started: Blastn
[2024-01-24 13:02:34,707] [INFO] Running command: blastn -query GCF_000327045.1_ASM32704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e4988de-4b0e-440d-9a1c-8d6f9f8c9f12/dqc_reference/reference_markers_gtdb.fasta -out GCF_000327045.1_ASM32704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:36,615] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:36,619] [INFO] Selected 18 target genomes.
[2024-01-24 13:02:36,620] [INFO] Target genome list was writen to GCF_000327045.1_ASM32704v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:36,634] [INFO] Task started: fastANI
[2024-01-24 13:02:36,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgd74e3302-d1a1-4247-937b-0d746501eb35/GCF_000327045.1_ASM32704v1_genomic.fna.gz --refList GCF_000327045.1_ASM32704v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000327045.1_ASM32704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:55,101] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:55,118] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:55,118] [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_000327045.1	s__Thioflavicoccus mobilis	100.0	1378	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thioflavicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016583835.1	s__Thiococcus pfennigii	85.9788	884	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiococcus	95.0	98.97	98.97	0.88	0.88	2	-
GCF_000224005.2	s__Marichromatium purpuratum	79.0252	399	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	78.8516	426	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_000585215.1	s__Imhoffiella purpurea	78.6596	415	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012276755.1	s__Marichromatium bheemlicum	78.5883	362	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018409545.1	s__Allochromatium tepidum	78.4958	337	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	78.3601	371	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_016584085.1	s__Halochromatium glycolicum	78.3029	377	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008632335.1	s__Thiohalocapsa marina	78.2675	335	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469165.1	s__Thiohalocapsa sp001469165	77.8424	395	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634315.1	s__Thiocapsa rosea	77.7746	352	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499735.1	s__Thiocapsa sp001499735	77.7508	347	1378	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	77.7231	349	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106925.1	s__Thiocapsa roseopersicina	77.6911	349	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813775.1	s__Thiodictyon syntrophicum	77.6293	362	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiodictyon	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903946935.1	s__Thiodictyon sp903946935	77.226	286	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiodictyon	95.0	99.93	99.89	0.97	0.96	5	-
GCA_903933125.1	s__Lamprocystis sp903933125	77.1841	256	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Lamprocystis	95.0	99.87	99.80	0.94	0.93	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:55,122] [INFO] GTDB search result was written to GCF_000327045.1_ASM32704v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:55,122] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:55,130] [INFO] DFAST_QC result json was written to GCF_000327045.1_ASM32704v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:55,131] [INFO] DFAST_QC completed!
[2024-01-24 13:02:55,131] [INFO] Total running time: 0h1m29s