[2024-01-24 14:06:44,432] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:44,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:44,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg60af8a6f-c7cc-4208-9ce3-41fcc373ce6e/dqc_reference
[2024-01-24 14:06:45,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:45,824] [INFO] Task started: Prodigal
[2024-01-24 14:06:45,824] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bf0f2f0-7809-40ad-9288-208afc1812d7/GCF_002310495.1_ASM231049v1_genomic.fna.gz | prodigal -d GCF_002310495.1_ASM231049v1_genomic.fna/cds.fna -a GCF_002310495.1_ASM231049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:13,315] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:13,316] [INFO] Task started: HMMsearch
[2024-01-24 14:07:13,316] [INFO] Running command: hmmsearch --tblout GCF_002310495.1_ASM231049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60af8a6f-c7cc-4208-9ce3-41fcc373ce6e/dqc_reference/reference_markers.hmm GCF_002310495.1_ASM231049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:13,648] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:13,649] [INFO] Found 6/6 markers.
[2024-01-24 14:07:13,693] [INFO] Query marker FASTA was written to GCF_002310495.1_ASM231049v1_genomic.fna/markers.fasta
[2024-01-24 14:07:13,694] [INFO] Task started: Blastn
[2024-01-24 14:07:13,694] [INFO] Running command: blastn -query GCF_002310495.1_ASM231049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60af8a6f-c7cc-4208-9ce3-41fcc373ce6e/dqc_reference/reference_markers.fasta -out GCF_002310495.1_ASM231049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:14,319] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:14,327] [INFO] Selected 18 target genomes.
[2024-01-24 14:07:14,328] [INFO] Target genome list was writen to GCF_002310495.1_ASM231049v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:14,398] [INFO] Task started: fastANI
[2024-01-24 14:07:14,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bf0f2f0-7809-40ad-9288-208afc1812d7/GCF_002310495.1_ASM231049v1_genomic.fna.gz --refList GCF_002310495.1_ASM231049v1_genomic.fna/target_genomes.txt --output GCF_002310495.1_ASM231049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:29,251] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:29,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60af8a6f-c7cc-4208-9ce3-41fcc373ce6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:29,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60af8a6f-c7cc-4208-9ce3-41fcc373ce6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:29,259] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:29,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:29,260] [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
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	100.0	1576	1576	95	conclusive
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	78.6271	343	1576	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	77.9357	259	1576	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	77.5323	221	1576	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	77.4043	143	1576	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	76.891	254	1576	95	below_threshold
Pelagicoccus enzymogenes	strain=NFK12	GCA_014803405.1	2773457	2773457	type	True	75.9186	106	1576	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	75.2418	70	1576	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:29,262] [INFO] DFAST Taxonomy check result was written to GCF_002310495.1_ASM231049v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:29,263] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:29,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:29,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60af8a6f-c7cc-4208-9ce3-41fcc373ce6e/dqc_reference/checkm_data
[2024-01-24 14:07:29,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:29,318] [INFO] Task started: CheckM
[2024-01-24 14:07:29,318] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002310495.1_ASM231049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002310495.1_ASM231049v1_genomic.fna/checkm_input GCF_002310495.1_ASM231049v1_genomic.fna/checkm_result
[2024-01-24 14:08:43,094] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:43,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:43,115] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:43,115] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:43,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002310495.1_ASM231049v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:43,116] [INFO] Task started: Blastn
[2024-01-24 14:08:43,116] [INFO] Running command: blastn -query GCF_002310495.1_ASM231049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60af8a6f-c7cc-4208-9ce3-41fcc373ce6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002310495.1_ASM231049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:43,986] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:43,989] [INFO] Selected 24 target genomes.
[2024-01-24 14:08:43,990] [INFO] Target genome list was writen to GCF_002310495.1_ASM231049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:44,010] [INFO] Task started: fastANI
[2024-01-24 14:08:44,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bf0f2f0-7809-40ad-9288-208afc1812d7/GCF_002310495.1_ASM231049v1_genomic.fna.gz --refList GCF_002310495.1_ASM231049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002310495.1_ASM231049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:02,220] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:02,241] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:02,241] [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_002310495.1	s__Nibricoccus aquaticus	100.0	1576	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Nibricoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007559335.1	s__Rariglobus hedericola	78.6695	339	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018239845.1	s__Opitutus sp018239845	78.4401	343	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876795.1	s__Rariglobus sp903876795	78.289	282	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002288455.1	s__ER46 sp002288455	78.2097	292	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721945.1	s__Nibricoccus sp016721945	78.1968	292	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Nibricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839035.1	s__Opi-474 sp903839035	78.1819	265	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.67	99.48	0.93	0.89	8	-
GCA_903948415.1	s__CAITWF01 sp903948415	78.1525	358	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904685.1	s__Rariglobus sp903904685	78.062	256	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	99.84	99.84	0.96	0.96	2	-
GCA_016715765.1	s__UBA2377 sp016715765	77.8681	256	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235555.1	s__ER46 sp016235555	77.7684	365	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650175.1	s__Ereboglobus sp001650175	77.7072	372	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Ereboglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881475.1	s__Opi-474 sp903881475	77.6179	243	1576	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_903877135.1	s__Opitutus sp903877135	77.5639	258	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	99.97	99.95	0.97	0.97	4	-
GCA_903862955.1	s__Opi-474 sp903862955	77.548	276	1576	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_003054665.1	s__EW11 sp003054665	77.3406	300	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__EW11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871755.1	s__UBA6669 sp016871755	77.1726	203	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862595.1	s__UBA6669 sp903862595	77.1322	157	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	99.22	99.13	0.81	0.80	3	-
GCA_903848965.1	s__ER46 sp903848965	76.7367	171	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879845.1	s__J108 sp014879845	76.6165	237	1576	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__J108	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:02,243] [INFO] GTDB search result was written to GCF_002310495.1_ASM231049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:02,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:02,247] [INFO] DFAST_QC result json was written to GCF_002310495.1_ASM231049v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:02,248] [INFO] DFAST_QC completed!
[2024-01-24 14:09:02,248] [INFO] Total running time: 0h2m18s