[2024-01-25 18:37:35,582] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:37:35,585] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:37:35,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg035c1537-d171-4a85-9f9b-fa340bb35407/dqc_reference
[2024-01-25 18:37:36,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:37:36,744] [INFO] Task started: Prodigal
[2024-01-25 18:37:36,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg105de69b-c8c9-4c23-8628-5037998a3c61/GCF_014646115.1_ASM1464611v1_genomic.fna.gz | prodigal -d GCF_014646115.1_ASM1464611v1_genomic.fna/cds.fna -a GCF_014646115.1_ASM1464611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:37:57,497] [INFO] Task succeeded: Prodigal
[2024-01-25 18:37:57,497] [INFO] Task started: HMMsearch
[2024-01-25 18:37:57,497] [INFO] Running command: hmmsearch --tblout GCF_014646115.1_ASM1464611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg035c1537-d171-4a85-9f9b-fa340bb35407/dqc_reference/reference_markers.hmm GCF_014646115.1_ASM1464611v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:37:57,799] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:37:57,800] [INFO] Found 6/6 markers.
[2024-01-25 18:37:57,861] [INFO] Query marker FASTA was written to GCF_014646115.1_ASM1464611v1_genomic.fna/markers.fasta
[2024-01-25 18:37:57,861] [INFO] Task started: Blastn
[2024-01-25 18:37:57,862] [INFO] Running command: blastn -query GCF_014646115.1_ASM1464611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg035c1537-d171-4a85-9f9b-fa340bb35407/dqc_reference/reference_markers.fasta -out GCF_014646115.1_ASM1464611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:37:59,201] [INFO] Task succeeded: Blastn
[2024-01-25 18:37:59,203] [INFO] Selected 28 target genomes.
[2024-01-25 18:37:59,204] [INFO] Target genome list was writen to GCF_014646115.1_ASM1464611v1_genomic.fna/target_genomes.txt
[2024-01-25 18:37:59,237] [INFO] Task started: fastANI
[2024-01-25 18:37:59,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg105de69b-c8c9-4c23-8628-5037998a3c61/GCF_014646115.1_ASM1464611v1_genomic.fna.gz --refList GCF_014646115.1_ASM1464611v1_genomic.fna/target_genomes.txt --output GCF_014646115.1_ASM1464611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:38:52,719] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:52,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg035c1537-d171-4a85-9f9b-fa340bb35407/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:38:52,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg035c1537-d171-4a85-9f9b-fa340bb35407/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:38:52,736] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:38:52,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:38:52,736] [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 camponoticapitis	strain=CGMCC 4.7275	GCA_014646115.1	1616125	1616125	type	True	100.0	2715	2718	95	conclusive
Streptomyces niveus	strain=NRRL 2466	GCA_001723055.1	193462	193462	type	True	90.2596	1820	2718	95	below_threshold
Streptomyces scopuliridis	strain=RB72	GCA_003073355.1	452529	452529	type	True	83.6345	1445	2718	95	below_threshold
Streptomyces scopuliridis	strain=NRRL B-24574	GCA_000718095.1	452529	452529	type	True	83.6004	1545	2718	95	below_threshold
Streptomyces odonnellii	strain=NRRL B-24891	GCA_000981895.1	1417980	1417980	type	True	83.0606	1371	2718	95	below_threshold
Streptomyces lunaelactis	strain=MM109	GCA_003054555.1	1535768	1535768	type	True	82.8954	1415	2718	95	below_threshold
Streptomyces chryseus	strain=DSM 40420	GCA_005981935.1	68186	68186	type	True	82.7635	1041	2718	95	below_threshold
Streptomyces chryseus	strain=JCM 4737	GCA_014650755.1	68186	68186	type	True	82.4718	1328	2718	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.3828	1380	2718	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	82.2309	1444	2718	95	below_threshold
Streptomyces badius	strain=JCM 4350	GCA_014649415.1	1941	1941	type	True	82.2019	1391	2718	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	82.1828	1184	2718	95	below_threshold
Streptomyces poriferorum	strain=P01-B04	GCA_019399235.1	2798799	2798799	type	True	82.108	1296	2718	95	below_threshold
[Kitasatospora] papulosa	strain=NRRL B-16504	GCA_000717245.1	1464011	1464011	type	True	81.7852	1318	2718	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	81.7336	1303	2718	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	81.6612	1362	2718	95	below_threshold
Streptomyces gardneri	strain=JCM 4375	GCA_014655085.1	66892	66892	type	True	81.5602	1336	2718	95	below_threshold
Streptomyces gardneri	strain=NBRC 12865	GCA_006539185.1	66892	66892	type	True	81.4891	1351	2718	95	below_threshold
Streptomyces kanasensis	strain=ZX01	GCA_001484625.1	936756	936756	type	True	81.3767	1215	2718	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	81.1907	1417	2718	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	80.8575	1184	2718	95	below_threshold
Streptomyces gougerotii	strain=JCM 4136	GCA_014648955.1	53448	53448	suspected-type	True	80.8274	1147	2718	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	80.7616	1184	2718	95	below_threshold
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	80.2312	1022	2718	95	below_threshold
Streptomyces sulfonofaciens	strain=JCM 5069	GCA_014656295.1	68272	68272	type	True	80.1469	1229	2718	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	80.062	983	2718	95	below_threshold
Streptomyces zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	79.4082	1013	2718	95	below_threshold
[Pseudopropionibacterium] massiliense	strain=Marseille-P6184	GCA_900607225.1	2220000	2220000	type	True	75.4851	119	2718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:38:52,738] [INFO] DFAST Taxonomy check result was written to GCF_014646115.1_ASM1464611v1_genomic.fna/tc_result.tsv
[2024-01-25 18:38:52,739] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:38:52,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:38:52,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg035c1537-d171-4a85-9f9b-fa340bb35407/dqc_reference/checkm_data
[2024-01-25 18:38:52,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:38:52,816] [INFO] Task started: CheckM
[2024-01-25 18:38:52,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646115.1_ASM1464611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646115.1_ASM1464611v1_genomic.fna/checkm_input GCF_014646115.1_ASM1464611v1_genomic.fna/checkm_result
[2024-01-25 18:40:12,214] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:12,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:12,239] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:12,239] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:12,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646115.1_ASM1464611v1_genomic.fna/markers.fasta)
[2024-01-25 18:40:12,241] [INFO] Task started: Blastn
[2024-01-25 18:40:12,241] [INFO] Running command: blastn -query GCF_014646115.1_ASM1464611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg035c1537-d171-4a85-9f9b-fa340bb35407/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646115.1_ASM1464611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:14,536] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:14,541] [INFO] Selected 18 target genomes.
[2024-01-25 18:40:14,541] [INFO] Target genome list was writen to GCF_014646115.1_ASM1464611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:14,550] [INFO] Task started: fastANI
[2024-01-25 18:40:14,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg105de69b-c8c9-4c23-8628-5037998a3c61/GCF_014646115.1_ASM1464611v1_genomic.fna.gz --refList GCF_014646115.1_ASM1464611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646115.1_ASM1464611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:40:49,805] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:49,816] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:40:49,817] [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_014646115.1	s__Streptomyces camponoticapitis	100.0	2715	2718	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_002009175.1	s__Streptomyces niveus_A	90.3131	1978	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001723055.1	s__Streptomyces niveus	90.2733	1818	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.45	97.47	0.93	0.91	3	-
GCF_010384365.1	s__Streptomyces sp010384365	90.0577	1993	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.09	98.09	0.85	0.85	2	-
GCF_000818175.1	s__Streptomyces sp000818175	83.0077	1507	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000818195.1	s__Streptomyces sp000818195	82.8017	1543	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003719395.1	s__Streptomyces altiplanensis	82.572	1300	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	96.26	0.83	0.83	2	-
GCF_900119365.1	s__Streptomyces atratus_B	82.2139	1383	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002711365.1	s__Streptomyces sp002711365	82.1593	1412	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	96.67	0.92	0.87	7	-
GCF_000373645.1	s__Streptomyces sp000373645	82.0858	1361	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000717595.1	s__Streptomyces flavochromogenes	81.5894	1350	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5951	N/A	N/A	N/A	N/A	1	-
GCF_009769735.1	s__Streptomyces sp009769735	81.0895	1401	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	80.9415	997	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	80.8097	1431	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045015.1	s__Streptomyces scabichelini	80.7548	1275	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017349075.1	s__Streptomyces triculaminicus_A	80.6673	1093	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.73	0.98	0.98	3	-
GCF_900110735.1	s__Streptomyces radiopugnans	80.2426	1020	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203645.1	s__Streptomyces zagrosensis	79.4251	1011	2718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:40:49,822] [INFO] GTDB search result was written to GCF_014646115.1_ASM1464611v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:40:49,827] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:40:49,835] [INFO] DFAST_QC result json was written to GCF_014646115.1_ASM1464611v1_genomic.fna/dqc_result.json
[2024-01-25 18:40:49,835] [INFO] DFAST_QC completed!
[2024-01-25 18:40:49,836] [INFO] Total running time: 0h3m14s