[2023-06-17 08:40:18,680] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:40:18,697] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:40:18,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg424b4ec7-68fb-409d-adad-6c6a92345d52/dqc_reference
[2023-06-17 08:40:20,531] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:40:20,532] [INFO] Task started: Prodigal
[2023-06-17 08:40:20,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fb73873-8c7e-4202-8ab0-dca905e3df71/GCA_009695065.1_ASM969506v1_genomic.fna.gz | prodigal -d GCA_009695065.1_ASM969506v1_genomic.fna/cds.fna -a GCA_009695065.1_ASM969506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:40:42,044] [INFO] Task succeeded: Prodigal
[2023-06-17 08:40:42,044] [INFO] Task started: HMMsearch
[2023-06-17 08:40:42,045] [INFO] Running command: hmmsearch --tblout GCA_009695065.1_ASM969506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg424b4ec7-68fb-409d-adad-6c6a92345d52/dqc_reference/reference_markers.hmm GCA_009695065.1_ASM969506v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:40:42,300] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:40:42,302] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4fb73873-8c7e-4202-8ab0-dca905e3df71/GCA_009695065.1_ASM969506v1_genomic.fna.gz]
[2023-06-17 08:40:42,353] [INFO] Query marker FASTA was written to GCA_009695065.1_ASM969506v1_genomic.fna/markers.fasta
[2023-06-17 08:40:42,354] [INFO] Task started: Blastn
[2023-06-17 08:40:42,354] [INFO] Running command: blastn -query GCA_009695065.1_ASM969506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg424b4ec7-68fb-409d-adad-6c6a92345d52/dqc_reference/reference_markers.fasta -out GCA_009695065.1_ASM969506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:40:42,972] [INFO] Task succeeded: Blastn
[2023-06-17 08:40:42,976] [INFO] Selected 8 target genomes.
[2023-06-17 08:40:42,976] [INFO] Target genome list was writen to GCA_009695065.1_ASM969506v1_genomic.fna/target_genomes.txt
[2023-06-17 08:40:42,979] [INFO] Task started: fastANI
[2023-06-17 08:40:42,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fb73873-8c7e-4202-8ab0-dca905e3df71/GCA_009695065.1_ASM969506v1_genomic.fna.gz --refList GCA_009695065.1_ASM969506v1_genomic.fna/target_genomes.txt --output GCA_009695065.1_ASM969506v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:40:50,248] [INFO] Task succeeded: fastANI
[2023-06-17 08:40:50,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg424b4ec7-68fb-409d-adad-6c6a92345d52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:40:50,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg424b4ec7-68fb-409d-adad-6c6a92345d52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:40:50,261] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 08:40:50,261] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 08:40:50,262] [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
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	77.51	199	1138	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.213	137	1138	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	77.1347	131	1138	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.9097	87	1138	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	76.68	95	1138	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	76.6301	90	1138	95	below_threshold
Streptomyces radicis	strain=DS1-2	GCA_003626575.1	1750517	1750517	type	True	74.5783	71	1138	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 08:40:50,264] [INFO] DFAST Taxonomy check result was written to GCA_009695065.1_ASM969506v1_genomic.fna/tc_result.tsv
[2023-06-17 08:40:50,264] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:40:50,264] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:40:50,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg424b4ec7-68fb-409d-adad-6c6a92345d52/dqc_reference/checkm_data
[2023-06-17 08:40:50,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:40:50,303] [INFO] Task started: CheckM
[2023-06-17 08:40:50,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009695065.1_ASM969506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009695065.1_ASM969506v1_genomic.fna/checkm_input GCA_009695065.1_ASM969506v1_genomic.fna/checkm_result
[2023-06-17 08:41:48,057] [INFO] Task succeeded: CheckM
[2023-06-17 08:41:48,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:41:48,082] [INFO] ===== Completeness check finished =====
[2023-06-17 08:41:48,082] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:41:48,083] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009695065.1_ASM969506v1_genomic.fna/markers.fasta)
[2023-06-17 08:41:48,083] [INFO] Task started: Blastn
[2023-06-17 08:41:48,083] [INFO] Running command: blastn -query GCA_009695065.1_ASM969506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg424b4ec7-68fb-409d-adad-6c6a92345d52/dqc_reference/reference_markers_gtdb.fasta -out GCA_009695065.1_ASM969506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:41:48,919] [INFO] Task succeeded: Blastn
[2023-06-17 08:41:48,938] [INFO] Selected 15 target genomes.
[2023-06-17 08:41:48,938] [INFO] Target genome list was writen to GCA_009695065.1_ASM969506v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:41:48,950] [INFO] Task started: fastANI
[2023-06-17 08:41:48,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fb73873-8c7e-4202-8ab0-dca905e3df71/GCA_009695065.1_ASM969506v1_genomic.fna.gz --refList GCA_009695065.1_ASM969506v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009695065.1_ASM969506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:42:00,508] [INFO] Task succeeded: fastANI
[2023-06-17 08:42:00,525] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 08:42:00,526] [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
GCA_009695065.1	s__ER46 sp009695065	100.0	1135	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	96.54	96.54	0.63	0.63	2	conclusive
GCA_903830425.1	s__Opi-474 sp903830425	78.5257	207	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.49	99.28	0.91	0.87	25	-
GCA_903855985.1	s__Opi-474 sp903855985	78.3972	230	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.84	99.84	0.94	0.94	2	-
GCA_903948415.1	s__CAITWF01 sp903948415	78.1624	320	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862955.1	s__Opi-474 sp903862955	78.1161	222	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.96	99.95	0.97	0.97	5	-
GCA_903881475.1	s__Opi-474 sp903881475	78.0975	219	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.50	98.31	0.92	0.83	9	-
GCA_903840415.1	s__CAITWF01 sp903840415	78.0126	244	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	99.98	99.98	0.98	0.97	3	-
GCA_016793535.1	s__ER46 sp016793535	77.9556	311	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209255.1	s__ER46 sp016209255	77.8019	335	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848965.1	s__ER46 sp903848965	77.6351	243	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304445.1	s__Tous-C4FEB sp002304445	77.4185	176	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	98.22	97.15	0.85	0.81	4	-
GCA_005792355.1	s__ER46 sp005792355	77.4063	318	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	99.97	99.97	0.97	0.97	2	-
GCA_016795545.1	s__Lacunisphaera sp016795545	77.1395	156	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016199925.1	s__JACQFT01 sp016199925	77.0157	154	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__JACQFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737275.1	s__Tous-C4FEB sp002737275	76.8253	135	1138	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 08:42:00,528] [INFO] GTDB search result was written to GCA_009695065.1_ASM969506v1_genomic.fna/result_gtdb.tsv
[2023-06-17 08:42:00,529] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:42:00,532] [INFO] DFAST_QC result json was written to GCA_009695065.1_ASM969506v1_genomic.fna/dqc_result.json
[2023-06-17 08:42:00,532] [INFO] DFAST_QC completed!
[2023-06-17 08:42:00,532] [INFO] Total running time: 0h1m42s