[2024-01-24 11:26:54,316] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b3eb311-dd11-48c8-801b-1ef74fe26142/dqc_reference
[2024-01-24 11:26:58,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,223] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg19da1098-e193-44bf-930f-00173cab5e91/GCF_014649095.1_ASM1464909v1_genomic.fna.gz | prodigal -d GCF_014649095.1_ASM1464909v1_genomic.fna/cds.fna -a GCF_014649095.1_ASM1464909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:16,347] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:16,347] [INFO] Task started: HMMsearch
[2024-01-24 11:27:16,347] [INFO] Running command: hmmsearch --tblout GCF_014649095.1_ASM1464909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b3eb311-dd11-48c8-801b-1ef74fe26142/dqc_reference/reference_markers.hmm GCF_014649095.1_ASM1464909v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:16,694] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:16,696] [INFO] Found 6/6 markers.
[2024-01-24 11:27:16,752] [INFO] Query marker FASTA was written to GCF_014649095.1_ASM1464909v1_genomic.fna/markers.fasta
[2024-01-24 11:27:16,753] [INFO] Task started: Blastn
[2024-01-24 11:27:16,753] [INFO] Running command: blastn -query GCF_014649095.1_ASM1464909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b3eb311-dd11-48c8-801b-1ef74fe26142/dqc_reference/reference_markers.fasta -out GCF_014649095.1_ASM1464909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:18,110] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:18,114] [INFO] Selected 15 target genomes.
[2024-01-24 11:27:18,114] [INFO] Target genome list was writen to GCF_014649095.1_ASM1464909v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:18,122] [INFO] Task started: fastANI
[2024-01-24 11:27:18,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg19da1098-e193-44bf-930f-00173cab5e91/GCF_014649095.1_ASM1464909v1_genomic.fna.gz --refList GCF_014649095.1_ASM1464909v1_genomic.fna/target_genomes.txt --output GCF_014649095.1_ASM1464909v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:49,449] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:49,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b3eb311-dd11-48c8-801b-1ef74fe26142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:49,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b3eb311-dd11-48c8-801b-1ef74fe26142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:49,464] [INFO] Found 15 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:27:49,465] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:49,465] [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
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	100.0	2329	2330	95	conclusive
Streptomyces cinereoruber	strain=ATCC 19740	GCA_009299385.1	67260	67260	type	True	99.999	2330	2330	95	conclusive
Streptomyces cinereoruber	strain=NRRL ISP-5012	GCA_014197485.1	67260	67260	type	True	99.9955	2324	2330	95	conclusive
Streptomyces cinereoruber	strain=DSM 41512	GCA_011758705.1	67260	67260	type	True	99.986	2313	2330	95	conclusive
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	99.9649	2303	2330	95	conclusive
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	89.3995	1715	2330	95	below_threshold
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	89.3948	1753	2330	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	89.3338	1740	2330	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	89.2555	1708	2330	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	89.2289	1712	2330	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	88.6966	1341	2330	95	below_threshold
Streptomyces wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	88.6352	1704	2330	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.4099	1392	2330	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	83.2902	1150	2330	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	81.7879	1369	2330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:49,467] [INFO] DFAST Taxonomy check result was written to GCF_014649095.1_ASM1464909v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:49,467] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:49,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:49,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b3eb311-dd11-48c8-801b-1ef74fe26142/dqc_reference/checkm_data
[2024-01-24 11:27:49,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:49,532] [INFO] Task started: CheckM
[2024-01-24 11:27:49,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649095.1_ASM1464909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649095.1_ASM1464909v1_genomic.fna/checkm_input GCF_014649095.1_ASM1464909v1_genomic.fna/checkm_result
[2024-01-24 11:29:10,838] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:10,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:29:10,864] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:10,864] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:10,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649095.1_ASM1464909v1_genomic.fna/markers.fasta)
[2024-01-24 11:29:10,865] [INFO] Task started: Blastn
[2024-01-24 11:29:10,865] [INFO] Running command: blastn -query GCF_014649095.1_ASM1464909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b3eb311-dd11-48c8-801b-1ef74fe26142/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649095.1_ASM1464909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:13,106] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:13,111] [INFO] Selected 16 target genomes.
[2024-01-24 11:29:13,111] [INFO] Target genome list was writen to GCF_014649095.1_ASM1464909v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:13,125] [INFO] Task started: fastANI
[2024-01-24 11:29:13,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg19da1098-e193-44bf-930f-00173cab5e91/GCF_014649095.1_ASM1464909v1_genomic.fna.gz --refList GCF_014649095.1_ASM1464909v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649095.1_ASM1464909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:46,377] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:46,395] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:46,395] [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
GCA_000716465.1	s__Streptomyces bikiniensis	95.8317	1913	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.67	95.67	0.86	0.82	10	conclusive
GCF_001280125.1	s__Streptomyces sp001280125	93.9959	1828	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.57	95.16	0.89	0.81	3	-
GCF_014648895.1	s__Streptomyces tanashiensis	89.4029	1714	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	97.78	0.91	0.91	2	-
GCF_000830005.1	s__Streptomyces vietnamensis	89.3771	1735	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105415.1	s__Streptomyces sp900105415	89.3514	1759	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_003386135.1	s__Streptomyces sp003386135	89.3018	1693	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCF_014649755.1	s__Streptomyces litmocidini	89.2922	1706	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
GCF_008639165.1	s__Streptomyces venezuelae	88.9665	1710	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	98.42	0.98	0.95	7	-
GCA_000717735.1	s__Streptomyces griseoluteus_A	88.9502	1683	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_000725545.1	s__Streptomyces exfoliatus	88.9491	1706	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_014656215.1	s__Streptomyces zaomyceticus	88.9098	1705	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539185.1	s__Streptomyces gardneri	88.651	1677	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.06	97.41	0.92	0.89	5	-
GCF_014451325.1	s__Streptomyces sp014451325	88.1151	1195	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008345.1	s__Streptomyces showdoensis	86.4395	1600	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002355495.1	s__Streptomyces laurentii	85.215	1529	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973465.1	s__Streptomyces sp008973465	82.181	1331	2330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:29:46,397] [INFO] GTDB search result was written to GCF_014649095.1_ASM1464909v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:46,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:46,401] [INFO] DFAST_QC result json was written to GCF_014649095.1_ASM1464909v1_genomic.fna/dqc_result.json
[2024-01-24 11:29:46,401] [INFO] DFAST_QC completed!
[2024-01-24 11:29:46,402] [INFO] Total running time: 0h2m52s