[2024-01-24 13:46:25,529] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,530] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg45d58ebb-f4f7-40af-8edb-e94038dfcf70/dqc_reference
[2024-01-24 13:46:26,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:26,787] [INFO] Task started: Prodigal
[2024-01-24 13:46:26,787] [INFO] Running command: gunzip -c /var/lib/cwl/stgba71db2b-bf3c-44c2-8294-3374aa638e31/GCF_000514435.1_ASM51443v1_genomic.fna.gz | prodigal -d GCF_000514435.1_ASM51443v1_genomic.fna/cds.fna -a GCF_000514435.1_ASM51443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:41,150] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:41,151] [INFO] Task started: HMMsearch
[2024-01-24 13:46:41,151] [INFO] Running command: hmmsearch --tblout GCF_000514435.1_ASM51443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45d58ebb-f4f7-40af-8edb-e94038dfcf70/dqc_reference/reference_markers.hmm GCF_000514435.1_ASM51443v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:41,499] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:41,501] [INFO] Found 6/6 markers.
[2024-01-24 13:46:41,552] [INFO] Query marker FASTA was written to GCF_000514435.1_ASM51443v1_genomic.fna/markers.fasta
[2024-01-24 13:46:41,552] [INFO] Task started: Blastn
[2024-01-24 13:46:41,552] [INFO] Running command: blastn -query GCF_000514435.1_ASM51443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d58ebb-f4f7-40af-8edb-e94038dfcf70/dqc_reference/reference_markers.fasta -out GCF_000514435.1_ASM51443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:42,931] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:42,936] [INFO] Selected 14 target genomes.
[2024-01-24 13:46:42,937] [INFO] Target genome list was writen to GCF_000514435.1_ASM51443v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:42,944] [INFO] Task started: fastANI
[2024-01-24 13:46:42,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgba71db2b-bf3c-44c2-8294-3374aa638e31/GCF_000514435.1_ASM51443v1_genomic.fna.gz --refList GCF_000514435.1_ASM51443v1_genomic.fna/target_genomes.txt --output GCF_000514435.1_ASM51443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:00,799] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:00,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45d58ebb-f4f7-40af-8edb-e94038dfcf70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:00,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45d58ebb-f4f7-40af-8edb-e94038dfcf70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:00,811] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:47:00,812] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:00,812] [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
Salinispora mooreana	strain=CNT-150	GCA_000514435.1	999545	999545	type	True	100.0	1590	1596	95	conclusive
Salinispora mooreana	strain=DSM 45549	GCA_000379065.1	999545	999545	type	True	99.9883	1596	1596	95	conclusive
Salinispora cortesiana	strain=CNY-202	GCA_000484695.1	1305843	1305843	type	True	93.9041	1310	1596	95	below_threshold
Salinispora fenicalii	strain=CNT-569	GCA_000514815.1	1137263	1137263	type	True	92.8321	1313	1596	95	below_threshold
Salinispora oceanensis	strain=CNT-138	GCA_000514455.1	1050199	1050199	type	True	92.7314	1305	1596	95	below_threshold
Salinispora oceanensis	strain=DSM 45547	GCA_000383575.1	1050199	1050199	type	True	92.7248	1298	1596	95	below_threshold
Salinispora pacifica	strain=CNR114	GCA_000514775.1	351187	351187	suspected-type	True	92.4893	1315	1596	95	below_threshold
Salinispora vitiensis	strain=CNT-148	GCA_000514675.1	999544	999544	type	True	92.2638	1251	1596	95	below_threshold
Salinispora vitiensis	strain=DSM 45548	GCA_000378825.1	999544	999544	type	True	92.1702	1253	1596	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	82.7663	785	1596	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	81.9822	828	1596	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	81.844	908	1596	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	81.6516	892	1596	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.3148	364	1596	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:00,814] [INFO] DFAST Taxonomy check result was written to GCF_000514435.1_ASM51443v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:00,815] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:00,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:00,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45d58ebb-f4f7-40af-8edb-e94038dfcf70/dqc_reference/checkm_data
[2024-01-24 13:47:00,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:00,870] [INFO] Task started: CheckM
[2024-01-24 13:47:00,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000514435.1_ASM51443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000514435.1_ASM51443v1_genomic.fna/checkm_input GCF_000514435.1_ASM51443v1_genomic.fna/checkm_result
[2024-01-24 13:47:44,335] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:44,336] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:44,355] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:44,356] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:44,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000514435.1_ASM51443v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:44,357] [INFO] Task started: Blastn
[2024-01-24 13:47:44,357] [INFO] Running command: blastn -query GCF_000514435.1_ASM51443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d58ebb-f4f7-40af-8edb-e94038dfcf70/dqc_reference/reference_markers_gtdb.fasta -out GCF_000514435.1_ASM51443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:46,101] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:46,105] [INFO] Selected 6 target genomes.
[2024-01-24 13:47:46,106] [INFO] Target genome list was writen to GCF_000514435.1_ASM51443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:46,117] [INFO] Task started: fastANI
[2024-01-24 13:47:46,117] [INFO] Running command: fastANI --query /var/lib/cwl/stgba71db2b-bf3c-44c2-8294-3374aa638e31/GCF_000514435.1_ASM51443v1_genomic.fna.gz --refList GCF_000514435.1_ASM51443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000514435.1_ASM51443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:54,585] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:54,597] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:54,598] [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_000379065.1	s__Micromonospora mooreana	99.9883	1596	1596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.98	95.97	0.92	0.83	3	conclusive
GCF_000484695.1	s__Micromonospora cortesiana	93.8985	1311	1596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000514815.1	s__Micromonospora fenicalii	92.8321	1313	1596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_000383575.1	s__Micromonospora oceanensis	92.7084	1300	1596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.54	95.98	0.89	0.84	12	-
GCF_000514775.1	s__Micromonospora pacifica	92.4814	1316	1596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.56	96.63	0.90	0.86	17	-
GCF_000378825.1	s__Micromonospora vitiensis	92.1702	1253	1596	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.04	95.56	0.89	0.83	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:54,601] [INFO] GTDB search result was written to GCF_000514435.1_ASM51443v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:54,601] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:54,605] [INFO] DFAST_QC result json was written to GCF_000514435.1_ASM51443v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:54,606] [INFO] DFAST_QC completed!
[2024-01-24 13:47:54,606] [INFO] Total running time: 0h1m29s