[2024-01-24 13:46:40,701] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:40,704] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:40,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg04cfec57-1f93-442c-8042-001da4155ffc/dqc_reference
[2024-01-24 13:46:42,077] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:42,078] [INFO] Task started: Prodigal
[2024-01-24 13:46:42,078] [INFO] Running command: gunzip -c /var/lib/cwl/stg77078327-7e53-4360-bc5c-0b0733e03457/GCF_006569185.2_ASM656918v2_genomic.fna.gz | prodigal -d GCF_006569185.2_ASM656918v2_genomic.fna/cds.fna -a GCF_006569185.2_ASM656918v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:02,169] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:02,169] [INFO] Task started: HMMsearch
[2024-01-24 13:47:02,169] [INFO] Running command: hmmsearch --tblout GCF_006569185.2_ASM656918v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04cfec57-1f93-442c-8042-001da4155ffc/dqc_reference/reference_markers.hmm GCF_006569185.2_ASM656918v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:02,516] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:02,517] [INFO] Found 6/6 markers.
[2024-01-24 13:47:02,570] [INFO] Query marker FASTA was written to GCF_006569185.2_ASM656918v2_genomic.fna/markers.fasta
[2024-01-24 13:47:02,571] [INFO] Task started: Blastn
[2024-01-24 13:47:02,571] [INFO] Running command: blastn -query GCF_006569185.2_ASM656918v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg04cfec57-1f93-442c-8042-001da4155ffc/dqc_reference/reference_markers.fasta -out GCF_006569185.2_ASM656918v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:03,292] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:03,298] [INFO] Selected 39 target genomes.
[2024-01-24 13:47:03,298] [INFO] Target genome list was writen to GCF_006569185.2_ASM656918v2_genomic.fna/target_genomes.txt
[2024-01-24 13:47:03,348] [INFO] Task started: fastANI
[2024-01-24 13:47:03,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg77078327-7e53-4360-bc5c-0b0733e03457/GCF_006569185.2_ASM656918v2_genomic.fna.gz --refList GCF_006569185.2_ASM656918v2_genomic.fna/target_genomes.txt --output GCF_006569185.2_ASM656918v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:32,466] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:32,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04cfec57-1f93-442c-8042-001da4155ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:32,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04cfec57-1f93-442c-8042-001da4155ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:32,486] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:32,486] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:32,486] [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
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	100.0	1966	1970	95	conclusive
Caldilinea aerophila	strain=DSM 14535	GCA_000281175.1	133453	133453	type	True	76.6077	197	1970	95	below_threshold
Aggregatilinea lenta	strain=MO-CFX2	GCA_003569045.1	913108	913108	type	True	75.5837	60	1970	95	below_threshold
Thermaerobacter subterraneus	strain=DSM 13965	GCA_000183545.3	175696	175696	type	True	75.3168	106	1970	95	below_threshold
Deinococcus ficus	strain=CC-FR2-10	GCA_003444775.1	317577	317577	type	True	75.1983	56	1970	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.137	131	1970	95	below_threshold
Roseomonas harenae	strain=CPCC 101081	GCA_009848505.1	2692566	2692566	type	True	75.1283	69	1970	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	75.0827	124	1970	95	below_threshold
Hymenobacter nivis	strain=NBRC 111535	GCA_003149515.1	1850093	1850093	type	True	75.0572	52	1970	95	below_threshold
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	74.9617	82	1970	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	74.9517	88	1970	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	74.9251	76	1970	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	74.883	76	1970	95	below_threshold
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	74.8331	73	1970	95	below_threshold
Actinomadura montaniterrae	strain=CYP1-1B	GCA_008923365.1	1803903	1803903	type	True	74.8094	89	1970	95	below_threshold
Hymenobacter coccineus	strain=CCM 8649	GCA_001816125.1	1908235	1908235	type	True	74.8081	57	1970	95	below_threshold
Actinomadura soli	strain=14C53	GCA_005889715.1	2508997	2508997	type	True	74.6575	84	1970	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:32,489] [INFO] DFAST Taxonomy check result was written to GCF_006569185.2_ASM656918v2_genomic.fna/tc_result.tsv
[2024-01-24 13:47:32,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:32,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:32,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04cfec57-1f93-442c-8042-001da4155ffc/dqc_reference/checkm_data
[2024-01-24 13:47:32,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:32,549] [INFO] Task started: CheckM
[2024-01-24 13:47:32,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006569185.2_ASM656918v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006569185.2_ASM656918v2_genomic.fna/checkm_input GCF_006569185.2_ASM656918v2_genomic.fna/checkm_result
[2024-01-24 13:48:25,632] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:25,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:25,649] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:25,650] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:25,650] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006569185.2_ASM656918v2_genomic.fna/markers.fasta)
[2024-01-24 13:48:25,651] [INFO] Task started: Blastn
[2024-01-24 13:48:25,651] [INFO] Running command: blastn -query GCF_006569185.2_ASM656918v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg04cfec57-1f93-442c-8042-001da4155ffc/dqc_reference/reference_markers_gtdb.fasta -out GCF_006569185.2_ASM656918v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:26,593] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:26,600] [INFO] Selected 26 target genomes.
[2024-01-24 13:48:26,600] [INFO] Target genome list was writen to GCF_006569185.2_ASM656918v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:26,670] [INFO] Task started: fastANI
[2024-01-24 13:48:26,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg77078327-7e53-4360-bc5c-0b0733e03457/GCF_006569185.2_ASM656918v2_genomic.fna.gz --refList GCF_006569185.2_ASM656918v2_genomic.fna/target_genomes_gtdb.txt --output GCF_006569185.2_ASM656918v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:48,154] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:48,169] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:48,170] [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_006569185.1	s__Litorilinea aerophila	100.0	1966	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Litorilinea	95.0	99.85	99.85	0.99	0.99	2	conclusive
GCA_015494005.1	s__S144-5 sp015494005	78.6256	401	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__S144-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018003515.1	s__JAGNDO01 sp018003515	77.2054	317	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JAGNDO01	95.0	99.87	99.85	0.92	0.92	4	-
GCF_000281175.1	s__Caldilinea aerophila	76.6077	197	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	97.04	95.81	0.94	0.92	4	-
GCA_003451595.1	s__Caldilinea sp003451595	76.5781	176	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	99.85	99.85	0.94	0.94	2	-
GCA_016199425.1	s__JACQGT01 sp016199425	76.4225	166	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JACQGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523365.1	s__Bin5 sp011523365	76.4028	128	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710365.1	s__Caldilinea sp016710365	76.3821	172	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861025.1	s__Caldilinea sp016861025	76.3726	183	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879855.1	s__Caldilinea sp014879855	76.3201	161	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002391565.1	s__Caldilinea sp002391565	76.2738	180	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	99.77	99.77	0.90	0.90	2	-
GCA_003577005.1	s__CFX5 sp003577005	76.1316	259	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__CFX5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842085.1	s__CG2-30-64-16 sp002842085	76.1128	93	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__CG2-30-64-16;f__CG2-30-64-16;g__CG2-30-64-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002068935.1	s__MWBF01 sp002068935	75.8063	120	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__CG2-30-64-16;f__CG2-30-64-16;g__MWBF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011388385.1	s__DRWE01 sp011388385	75.5048	81	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__SpSt-313;f__SpSt-313;g__DRWE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237545.1	s__Promineofilum sp014237545	75.3061	69	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Promineofilales;f__Promineofilaceae;g__Promineofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002329325.1	s__UBA1429 sp002329325	75.2468	78	1970	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__UBA1429;f__UBA1429;g__UBA1429	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:48,171] [INFO] GTDB search result was written to GCF_006569185.2_ASM656918v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:48,172] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:48,179] [INFO] DFAST_QC result json was written to GCF_006569185.2_ASM656918v2_genomic.fna/dqc_result.json
[2024-01-24 13:48:48,179] [INFO] DFAST_QC completed!
[2024-01-24 13:48:48,180] [INFO] Total running time: 0h2m7s