[2024-01-25 19:35:35,507] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:35,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:35,508] [INFO] DQC Reference Directory: /var/lib/cwl/stgb07a7d0b-97f1-4d8c-8fd5-fca7d6ca830e/dqc_reference
[2024-01-25 19:35:36,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:36,634] [INFO] Task started: Prodigal
[2024-01-25 19:35:36,634] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3fd0a9d-3a9b-4770-a722-6caad8a622fd/GCF_014493765.1_ASM1449376v1_genomic.fna.gz | prodigal -d GCF_014493765.1_ASM1449376v1_genomic.fna/cds.fna -a GCF_014493765.1_ASM1449376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:02,492] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:02,492] [INFO] Task started: HMMsearch
[2024-01-25 19:36:02,492] [INFO] Running command: hmmsearch --tblout GCF_014493765.1_ASM1449376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb07a7d0b-97f1-4d8c-8fd5-fca7d6ca830e/dqc_reference/reference_markers.hmm GCF_014493765.1_ASM1449376v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:02,888] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:02,889] [INFO] Found 6/6 markers.
[2024-01-25 19:36:02,960] [INFO] Query marker FASTA was written to GCF_014493765.1_ASM1449376v1_genomic.fna/markers.fasta
[2024-01-25 19:36:02,960] [INFO] Task started: Blastn
[2024-01-25 19:36:02,960] [INFO] Running command: blastn -query GCF_014493765.1_ASM1449376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb07a7d0b-97f1-4d8c-8fd5-fca7d6ca830e/dqc_reference/reference_markers.fasta -out GCF_014493765.1_ASM1449376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:04,235] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:04,238] [INFO] Selected 23 target genomes.
[2024-01-25 19:36:04,238] [INFO] Target genome list was writen to GCF_014493765.1_ASM1449376v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:04,277] [INFO] Task started: fastANI
[2024-01-25 19:36:04,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3fd0a9d-3a9b-4770-a722-6caad8a622fd/GCF_014493765.1_ASM1449376v1_genomic.fna.gz --refList GCF_014493765.1_ASM1449376v1_genomic.fna/target_genomes.txt --output GCF_014493765.1_ASM1449376v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:52,125] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:52,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb07a7d0b-97f1-4d8c-8fd5-fca7d6ca830e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:52,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb07a7d0b-97f1-4d8c-8fd5-fca7d6ca830e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:52,139] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:36:52,139] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:36:52,139] [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 polyasparticus	strain=TRM66268-LWL	GCA_014493765.1	2767826	2767826	type	True	100.0	3307	3312	95	conclusive
Streptomyces mesophilus	strain=YC504	GCA_011044995.1	1775132	1775132	type	True	89.9512	2192	3312	95	below_threshold
Streptomyces boluensis	strain=YC537	GCA_009908195.1	1775135	1775135	type	True	82.8877	1416	3312	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	82.392	1443	3312	95	below_threshold
Streptomyces aureoverticillatus	strain=JCM 4347	GCA_014649395.1	66871	66871	type	True	81.9903	1634	3312	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	81.9484	1698	3312	95	below_threshold
Streptomyces xanthii	strain=CRXT-Y-14	GCA_014621695.1	2768069	2768069	type	True	81.9341	1567	3312	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_014650815.1	68200	68200	type	True	81.8795	1633	3312	95	below_threshold
Streptomyces alboflavus	strain=NRRL B-2373	GCA_000716675.1	67267	67267	type	True	81.8668	1631	3312	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_016411765.1	68200	68200	type	True	81.8574	1636	3312	95	below_threshold
Streptomyces triticagri	strain=NEAU-YY421	GCA_003429565.1	2293568	2293568	type	True	81.8219	1493	3312	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	81.6814	1622	3312	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	81.3832	1646	3312	95	below_threshold
Streptomyces lateritius	strain=JCM 4389	GCA_014649715.1	67313	67313	type	True	81.3742	1385	3312	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.2013	1399	3312	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	81.1911	1561	3312	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	81.1622	1568	3312	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	81.1577	1395	3312	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	81.1098	1333	3312	95	below_threshold
Streptomyces griseoluteus	strain=JCM 4765	GCA_004784465.1	29306	29306	type	True	81.0044	1253	3312	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	80.9615	1605	3312	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_000715845.1	371720	371720	type	True	80.4695	1292	3312	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	80.3585	1323	3312	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:52,141] [INFO] DFAST Taxonomy check result was written to GCF_014493765.1_ASM1449376v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:52,141] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:52,142] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:52,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb07a7d0b-97f1-4d8c-8fd5-fca7d6ca830e/dqc_reference/checkm_data
[2024-01-25 19:36:52,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:52,240] [INFO] Task started: CheckM
[2024-01-25 19:36:52,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014493765.1_ASM1449376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014493765.1_ASM1449376v1_genomic.fna/checkm_input GCF_014493765.1_ASM1449376v1_genomic.fna/checkm_result
[2024-01-25 19:39:26,024] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:26,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:26,049] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:26,049] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:26,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014493765.1_ASM1449376v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:26,050] [INFO] Task started: Blastn
[2024-01-25 19:39:26,050] [INFO] Running command: blastn -query GCF_014493765.1_ASM1449376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb07a7d0b-97f1-4d8c-8fd5-fca7d6ca830e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014493765.1_ASM1449376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:28,110] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:28,113] [INFO] Selected 13 target genomes.
[2024-01-25 19:39:28,113] [INFO] Target genome list was writen to GCF_014493765.1_ASM1449376v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:28,145] [INFO] Task started: fastANI
[2024-01-25 19:39:28,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3fd0a9d-3a9b-4770-a722-6caad8a622fd/GCF_014493765.1_ASM1449376v1_genomic.fna.gz --refList GCF_014493765.1_ASM1449376v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014493765.1_ASM1449376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:00,485] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:00,493] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:00,494] [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_014493765.1	s__Streptomyces polyasparticus	100.0	3307	3312	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_011044995.1	s__Streptomyces mesophilus	89.9464	2192	3312	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.86	0.86	2	-
GCA_000721375.1	s__Streptomyces sp000721375	88.2369	2358	3312	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100315.1	s__Streptomyces indicus	87.8791	2204	3312	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556545.1	s__Streptomyces formicae	82.0835	1688	3312	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003945545.1	s__Streptomyces sp003945545	82.0779	1543	3312	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000414115.1	s__Streptomyces aurantiacus_A	82.0297	1448	3312	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649395.1	s__Streptomyces aureoverticillatus	81.9491	1644	3312	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716675.1	s__Streptomyces alboflavus	81.7758	1652	3312	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.12	98.24	0.94	0.89	5	-
GCF_000373565.1	s__Streptomyces sp000373565	81.7027	1720	3312	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002005565.1	s__Streptomyces sp002005565	81.5959	1335	3312	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	81.4132	1709	3312	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103585.1	s__Streptomyces sp900103585	81.331	1617	3312	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 19:40:00,495] [INFO] GTDB search result was written to GCF_014493765.1_ASM1449376v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:00,496] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:00,503] [INFO] DFAST_QC result json was written to GCF_014493765.1_ASM1449376v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:00,503] [INFO] DFAST_QC completed!
[2024-01-25 19:40:00,503] [INFO] Total running time: 0h4m25s