[2024-01-24 14:07:29,934] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:29,938] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:29,938] [INFO] DQC Reference Directory: /var/lib/cwl/stg31f5c504-c321-4ff4-b60e-5f60c8eb4292/dqc_reference
[2024-01-24 14:07:31,224] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:31,225] [INFO] Task started: Prodigal
[2024-01-24 14:07:31,225] [INFO] Running command: gunzip -c /var/lib/cwl/stg9487e58d-5ab2-4331-a2d8-a88eab9eda85/GCF_012034205.1_ASM1203420v1_genomic.fna.gz | prodigal -d GCF_012034205.1_ASM1203420v1_genomic.fna/cds.fna -a GCF_012034205.1_ASM1203420v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:49,505] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:49,506] [INFO] Task started: HMMsearch
[2024-01-24 14:07:49,506] [INFO] Running command: hmmsearch --tblout GCF_012034205.1_ASM1203420v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31f5c504-c321-4ff4-b60e-5f60c8eb4292/dqc_reference/reference_markers.hmm GCF_012034205.1_ASM1203420v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:49,843] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:49,844] [INFO] Found 6/6 markers.
[2024-01-24 14:07:49,899] [INFO] Query marker FASTA was written to GCF_012034205.1_ASM1203420v1_genomic.fna/markers.fasta
[2024-01-24 14:07:49,900] [INFO] Task started: Blastn
[2024-01-24 14:07:49,900] [INFO] Running command: blastn -query GCF_012034205.1_ASM1203420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31f5c504-c321-4ff4-b60e-5f60c8eb4292/dqc_reference/reference_markers.fasta -out GCF_012034205.1_ASM1203420v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:51,303] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:51,308] [INFO] Selected 19 target genomes.
[2024-01-24 14:07:51,308] [INFO] Target genome list was writen to GCF_012034205.1_ASM1203420v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:51,321] [INFO] Task started: fastANI
[2024-01-24 14:07:51,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg9487e58d-5ab2-4331-a2d8-a88eab9eda85/GCF_012034205.1_ASM1203420v1_genomic.fna.gz --refList GCF_012034205.1_ASM1203420v1_genomic.fna/target_genomes.txt --output GCF_012034205.1_ASM1203420v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:08:27,891] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:27,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31f5c504-c321-4ff4-b60e-5f60c8eb4292/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:08:27,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31f5c504-c321-4ff4-b60e-5f60c8eb4292/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:08:27,912] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:08:27,912] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:08:27,912] [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 griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	87.3111	1626	2130	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	87.2587	1665	2130	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	86.9968	1301	2130	95	below_threshold
Streptomyces capillispiralis	strain=DSM 41695	GCA_007829875.1	68182	68182	type	True	86.8794	1656	2130	95	below_threshold
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	86.8747	1657	2130	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	86.841	1635	2130	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	86.8314	1629	2130	95	below_threshold
Streptomyces malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	86.6501	1645	2130	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	86.4677	1598	2130	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.7777	1613	2130	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.6109	1577	2130	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.4462	1315	2130	95	below_threshold
Streptomyces djakartensis	strain=JCM 4957	GCA_014651075.1	68193	68193	type	True	85.3823	1505	2130	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	85.3814	1510	2130	95	below_threshold
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	85.0651	1544	2130	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	84.8739	1575	2130	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.8483	1410	2130	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	84.6004	1533	2130	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	84.3957	1307	2130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:08:27,915] [INFO] DFAST Taxonomy check result was written to GCF_012034205.1_ASM1203420v1_genomic.fna/tc_result.tsv
[2024-01-24 14:08:27,916] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:08:27,916] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:08:27,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31f5c504-c321-4ff4-b60e-5f60c8eb4292/dqc_reference/checkm_data
[2024-01-24 14:08:27,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:08:28,003] [INFO] Task started: CheckM
[2024-01-24 14:08:28,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012034205.1_ASM1203420v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012034205.1_ASM1203420v1_genomic.fna/checkm_input GCF_012034205.1_ASM1203420v1_genomic.fna/checkm_result
[2024-01-24 14:10:00,178] [INFO] Task succeeded: CheckM
[2024-01-24 14:10:00,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:10:00,210] [INFO] ===== Completeness check finished =====
[2024-01-24 14:10:00,211] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:10:00,211] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012034205.1_ASM1203420v1_genomic.fna/markers.fasta)
[2024-01-24 14:10:00,212] [INFO] Task started: Blastn
[2024-01-24 14:10:00,212] [INFO] Running command: blastn -query GCF_012034205.1_ASM1203420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31f5c504-c321-4ff4-b60e-5f60c8eb4292/dqc_reference/reference_markers_gtdb.fasta -out GCF_012034205.1_ASM1203420v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:02,346] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:02,352] [INFO] Selected 20 target genomes.
[2024-01-24 14:10:02,352] [INFO] Target genome list was writen to GCF_012034205.1_ASM1203420v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:10:02,385] [INFO] Task started: fastANI
[2024-01-24 14:10:02,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg9487e58d-5ab2-4331-a2d8-a88eab9eda85/GCF_012034205.1_ASM1203420v1_genomic.fna.gz --refList GCF_012034205.1_ASM1203420v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012034205.1_ASM1203420v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:10:38,437] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:38,458] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:10:38,458] [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_012034205.1	s__Streptomyces sp012034205	100.0	2125	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009852415.1	s__Streptomyces sp009852415	87.3028	1636	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	87.2566	1665	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_008704515.1	s__Streptomyces viridosporus	87.1441	1521	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	99.12	0.96	0.94	4	-
GCF_007829875.1	s__Streptomyces capillispiralis	86.8794	1656	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001905725.1	s__Streptomyces sp001905725	86.8718	1637	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650055.1	s__Streptomyces malachitofuscus	86.6642	1643	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014655195.1	s__Streptomyces cellulosae	86.5588	1607	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.87	0.87	0.85	11	-
GCA_014650475.1	s__Streptomyces albogriseolus	86.5424	1595	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.59	97.23	0.93	0.90	7	-
GCF_014649995.1	s__Streptomyces griseoflavus	86.4719	1597	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002154585.1	s__Streptomyces pseudogriseolus	86.4217	1350	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.58	96.58	0.90	0.87	9	-
GCF_002899455.1	s__Streptomyces sp002899455	86.4066	1526	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649355.1	s__Streptomyces althioticus	86.3893	1588	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.43	96.72	0.91	0.83	9	-
GCA_014649575.1	s__Streptomyces griseoincarnatus	86.2662	1601	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.24	97.52	0.91	0.85	21	-
GCA_003248315.1	s__Streptomyces sp003248315	85.7843	1572	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651075.1	s__Streptomyces djakartensis	85.359	1509	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002155895.1	s__Streptomyces rochei	85.3211	1357	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.80	98.25	0.91	0.79	28	-
GCF_002920535.1	s__Streptomyces sp002920535	85.2533	1522	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383935.1	s__Streptomyces sp000383935	84.763	1477	2130	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	-
GCF_016741775.1	s__Streptomyces actinomycinicus	84.5205	1484	2130	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 14:10:38,460] [INFO] GTDB search result was written to GCF_012034205.1_ASM1203420v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:10:38,460] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:10:38,464] [INFO] DFAST_QC result json was written to GCF_012034205.1_ASM1203420v1_genomic.fna/dqc_result.json
[2024-01-24 14:10:38,464] [INFO] DFAST_QC completed!
[2024-01-24 14:10:38,464] [INFO] Total running time: 0h3m9s