[2024-01-24 10:57:26,549] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,552] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0c09bc3-b243-4cbd-9792-f05c8540ccce/dqc_reference
[2024-01-24 10:57:27,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:27,963] [INFO] Task started: Prodigal
[2024-01-24 10:57:27,963] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc7ef0e3-426a-4b67-980d-2f512b83c63d/GCF_014650775.1_ASM1465077v1_genomic.fna.gz | prodigal -d GCF_014650775.1_ASM1465077v1_genomic.fna/cds.fna -a GCF_014650775.1_ASM1465077v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:47,469] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:47,470] [INFO] Task started: HMMsearch
[2024-01-24 10:57:47,470] [INFO] Running command: hmmsearch --tblout GCF_014650775.1_ASM1465077v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0c09bc3-b243-4cbd-9792-f05c8540ccce/dqc_reference/reference_markers.hmm GCF_014650775.1_ASM1465077v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:47,838] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:47,840] [INFO] Found 6/6 markers.
[2024-01-24 10:57:47,895] [INFO] Query marker FASTA was written to GCF_014650775.1_ASM1465077v1_genomic.fna/markers.fasta
[2024-01-24 10:57:47,895] [INFO] Task started: Blastn
[2024-01-24 10:57:47,895] [INFO] Running command: blastn -query GCF_014650775.1_ASM1465077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0c09bc3-b243-4cbd-9792-f05c8540ccce/dqc_reference/reference_markers.fasta -out GCF_014650775.1_ASM1465077v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:49,191] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:49,195] [INFO] Selected 21 target genomes.
[2024-01-24 10:57:49,195] [INFO] Target genome list was writen to GCF_014650775.1_ASM1465077v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:49,203] [INFO] Task started: fastANI
[2024-01-24 10:57:49,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc7ef0e3-426a-4b67-980d-2f512b83c63d/GCF_014650775.1_ASM1465077v1_genomic.fna.gz --refList GCF_014650775.1_ASM1465077v1_genomic.fna/target_genomes.txt --output GCF_014650775.1_ASM1465077v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:31,428] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:31,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0c09bc3-b243-4cbd-9792-f05c8540ccce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:31,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0c09bc3-b243-4cbd-9792-f05c8540ccce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:31,444] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:31,445] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:31,445] [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 cirratus	strain=JCM 4738	GCA_014650775.1	68187	68187	type	True	100.0	2394	2395	95	conclusive
Streptomyces vinaceus	strain=ATCC 27476	GCA_008704935.1	1960	1960	type	True	87.1257	1703	2395	95	below_threshold
Streptomyces goshikiensis	strain=JCM 4640	GCA_014650555.1	1942	1942	type	True	87.0025	1713	2395	95	below_threshold
Streptomyces vinaceus	strain=JCM 4849	GCA_014656155.1	1960	1960	type	True	86.963	1708	2395	95	below_threshold
Streptomyces katrae	strain=NRRL ISP-5550	GCA_000966975.1	68223	68223	type	True	86.695	1328	2395	95	below_threshold
Streptomyces xanthophaeus	strain=NBRC 12829	GCA_016755895.1	67385	67385	type	True	86.6361	1686	2395	95	below_threshold
Streptomyces xanthophaeus	strain=NRRL B-5414	GCA_000725805.1	67385	67385	type	True	86.63	1686	2395	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_014648615.1	66374	66374	type	True	86.5991	1711	2395	95	below_threshold
Streptomyces nojiriensis	strain=NBRC 13794	GCA_016755855.1	66374	66374	type	True	86.5836	1723	2395	95	below_threshold
Streptomyces spororaveus	strain=NBRC 15456	GCA_016755875.1	284039	284039	type	True	86.5467	1706	2395	95	below_threshold
Streptomyces nojiriensis	strain=JCM 3382	GCA_017639205.1	66374	66374	type	True	86.5465	1736	2395	95	below_threshold
Streptomyces avidinii	strain=JCM 4726	GCA_014650695.1	1895	1895	type	True	86.5326	1694	2395	95	below_threshold
Streptomyces avidinii	strain=DSM 40526	GCA_017874515.1	1895	1895	type	True	86.4702	1698	2395	95	below_threshold
Streptomyces amritsarensis	strain=MTCC 11845	GCA_001953875.1	681158	681158	type	True	86.3689	1609	2395	95	below_threshold
Streptomyces virginiae	strain=NRRL ISP-5094	GCA_000720455.1	1961	1961	suspected-type	True	86.3637	1688	2395	95	below_threshold
Streptomyces subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	86.3266	1621	2395	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	81.8617	1066	2395	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	81.2934	1197	2395	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.0877	1109	2395	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	81.0527	1262	2395	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.6187	1120	2395	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:31,446] [INFO] DFAST Taxonomy check result was written to GCF_014650775.1_ASM1465077v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:31,447] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:31,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:31,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0c09bc3-b243-4cbd-9792-f05c8540ccce/dqc_reference/checkm_data
[2024-01-24 10:58:31,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:31,511] [INFO] Task started: CheckM
[2024-01-24 10:58:31,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650775.1_ASM1465077v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650775.1_ASM1465077v1_genomic.fna/checkm_input GCF_014650775.1_ASM1465077v1_genomic.fna/checkm_result
[2024-01-24 11:00:01,516] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:01,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:01,534] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:01,535] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:01,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650775.1_ASM1465077v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:01,535] [INFO] Task started: Blastn
[2024-01-24 11:00:01,535] [INFO] Running command: blastn -query GCF_014650775.1_ASM1465077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0c09bc3-b243-4cbd-9792-f05c8540ccce/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650775.1_ASM1465077v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:03,520] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:03,523] [INFO] Selected 18 target genomes.
[2024-01-24 11:00:03,523] [INFO] Target genome list was writen to GCF_014650775.1_ASM1465077v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:03,535] [INFO] Task started: fastANI
[2024-01-24 11:00:03,535] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc7ef0e3-426a-4b67-980d-2f512b83c63d/GCF_014650775.1_ASM1465077v1_genomic.fna.gz --refList GCF_014650775.1_ASM1465077v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650775.1_ASM1465077v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:37,522] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:37,536] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:37,536] [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_014650775.1	s__Streptomyces cirratus	100.0	2394	2395	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_004795055.1	s__Streptomyces sp004795055	91.4437	1920	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717915.1	s__Streptomyces sp000717915	87.5133	1596	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.92	95.47	0.90	0.89	4	-
GCF_018614095.1	s__Streptomyces sp018614095	87.4413	1609	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.34	0.93	0.89	3	-
GCF_001279725.1	s__Streptomyces sp001279725	87.2545	1574	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704935.1	s__Streptomyces vinaceus	87.1288	1701	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.65	97.63	0.95	0.92	5	-
GCF_000720145.1	s__Streptomyces sp000720145	87.0856	1660	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717655.1	s__Streptomyces katrae_B	87.0564	1690	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.60	96.50	0.86	0.86	4	-
GCF_018614075.1	s__Streptomyces sp018614075	87.0309	1576	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614155.1	s__Streptomyces sp018614155	86.9477	1620	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803845.1	s__Streptomyces lavendulae_C	86.8328	1805	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.97	0.99	0.99	3	-
GCF_001746425.1	s__Streptomyces subrutilus_A	86.7846	1652	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003950035.1	s__Streptomyces sp000158895	86.7274	1730	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.52	95.50	0.87	0.87	3	-
GCF_018614195.1	s__Streptomyces sp018614195	86.7125	1611	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002028425.1	s__Streptomyces katrae_A	86.685	1755	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.60	99.44	0.97	0.94	4	-
GCF_000725805.1	s__Streptomyces xanthophaeus	86.6314	1686	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.79	99.60	0.97	0.96	3	-
GCF_018614135.1	s__Streptomyces sp018614135	86.38	1508	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953875.1	s__Streptomyces amritsarensis	86.3429	1612	2395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	98.97	0.95	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:37,537] [INFO] GTDB search result was written to GCF_014650775.1_ASM1465077v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:37,538] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:37,541] [INFO] DFAST_QC result json was written to GCF_014650775.1_ASM1465077v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:37,542] [INFO] DFAST_QC completed!
[2024-01-24 11:00:37,542] [INFO] Total running time: 0h3m11s