[2024-01-24 13:37:41,576] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:41,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:41,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fe58a12-bb86-487e-80bf-5b9b891a4b9b/dqc_reference
[2024-01-24 13:37:42,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:42,692] [INFO] Task started: Prodigal
[2024-01-24 13:37:42,692] [INFO] Running command: gunzip -c /var/lib/cwl/stge6feed2a-3f2e-42e9-a02a-9a79f5a000c6/GCF_014202875.1_ASM1420287v1_genomic.fna.gz | prodigal -d GCF_014202875.1_ASM1420287v1_genomic.fna/cds.fna -a GCF_014202875.1_ASM1420287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:51,974] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:51,975] [INFO] Task started: HMMsearch
[2024-01-24 13:37:51,975] [INFO] Running command: hmmsearch --tblout GCF_014202875.1_ASM1420287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fe58a12-bb86-487e-80bf-5b9b891a4b9b/dqc_reference/reference_markers.hmm GCF_014202875.1_ASM1420287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:52,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:52,356] [INFO] Found 6/6 markers.
[2024-01-24 13:37:52,396] [INFO] Query marker FASTA was written to GCF_014202875.1_ASM1420287v1_genomic.fna/markers.fasta
[2024-01-24 13:37:52,396] [INFO] Task started: Blastn
[2024-01-24 13:37:52,396] [INFO] Running command: blastn -query GCF_014202875.1_ASM1420287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fe58a12-bb86-487e-80bf-5b9b891a4b9b/dqc_reference/reference_markers.fasta -out GCF_014202875.1_ASM1420287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:52,991] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:52,994] [INFO] Selected 20 target genomes.
[2024-01-24 13:37:52,994] [INFO] Target genome list was writen to GCF_014202875.1_ASM1420287v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:53,000] [INFO] Task started: fastANI
[2024-01-24 13:37:53,000] [INFO] Running command: fastANI --query /var/lib/cwl/stge6feed2a-3f2e-42e9-a02a-9a79f5a000c6/GCF_014202875.1_ASM1420287v1_genomic.fna.gz --refList GCF_014202875.1_ASM1420287v1_genomic.fna/target_genomes.txt --output GCF_014202875.1_ASM1420287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:08,957] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:08,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fe58a12-bb86-487e-80bf-5b9b891a4b9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:08,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fe58a12-bb86-487e-80bf-5b9b891a4b9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:08,965] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:38:08,965] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:08,965] [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
Anaerocolumna cellulosilytica	strain=DSM 100423	GCA_014202875.1	433286	433286	type	True	100.0	1745	1748	95	conclusive
Anaerocolumna cellulosilytica	strain=SN021	GCA_014218335.1	433286	433286	type	True	99.998	1748	1748	95	conclusive
Anaerocolumna sedimenticola	strain=CBA3638	GCA_009931695.1	2696063	2696063	type	True	78.0864	275	1748	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	77.8185	176	1748	95	below_threshold
Anaerocolumna jejuensis	strain=DSM 15929	GCA_900142215.1	259063	259063	type	True	77.5795	213	1748	95	below_threshold
Anaerocolumna xylanovorans	strain=DSM 12503	GCA_900143645.1	100134	100134	type	True	77.485	192	1748	95	below_threshold
Anaerocolumna chitinilytica	strain=CTTW	GCA_014218355.1	1727145	1727145	type	True	77.4282	204	1748	95	below_threshold
Anaerosporobacter mobilis	strain=DSM 15930	GCA_900142955.1	264463	264463	type	True	77.4035	79	1748	95	below_threshold
Mobilisporobacter senegalensis	strain=DSM 26537	GCA_003752155.1	1329262	1329262	type	True	77.2058	97	1748	95	below_threshold
Mobilitalea sibirica	strain=DSM 26468	GCA_015999265.1	1462919	1462919	type	True	76.6564	91	1748	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:08,967] [INFO] DFAST Taxonomy check result was written to GCF_014202875.1_ASM1420287v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:08,967] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:08,967] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:08,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fe58a12-bb86-487e-80bf-5b9b891a4b9b/dqc_reference/checkm_data
[2024-01-24 13:38:08,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:09,019] [INFO] Task started: CheckM
[2024-01-24 13:38:09,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202875.1_ASM1420287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202875.1_ASM1420287v1_genomic.fna/checkm_input GCF_014202875.1_ASM1420287v1_genomic.fna/checkm_result
[2024-01-24 13:38:39,114] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:39,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:39,140] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:39,141] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:39,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202875.1_ASM1420287v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:39,141] [INFO] Task started: Blastn
[2024-01-24 13:38:39,141] [INFO] Running command: blastn -query GCF_014202875.1_ASM1420287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fe58a12-bb86-487e-80bf-5b9b891a4b9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202875.1_ASM1420287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:40,069] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:40,071] [INFO] Selected 19 target genomes.
[2024-01-24 13:38:40,072] [INFO] Target genome list was writen to GCF_014202875.1_ASM1420287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:40,085] [INFO] Task started: fastANI
[2024-01-24 13:38:40,085] [INFO] Running command: fastANI --query /var/lib/cwl/stge6feed2a-3f2e-42e9-a02a-9a79f5a000c6/GCF_014202875.1_ASM1420287v1_genomic.fna.gz --refList GCF_014202875.1_ASM1420287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202875.1_ASM1420287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:53,777] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:53,787] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:53,787] [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_014218335.1	s__Anaerocolumna cellulosilytica	99.998	1748	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000702945.1	s__Anaerocolumna sp000702945	78.3224	254	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434335.1	s__Anaerocolumna sp002434335	78.1039	223	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.22	99.22	0.91	0.91	2	-
GCF_009931695.1	s__Anaerocolumna sedimenticola	78.0738	276	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115365.1	s__Anaerocolumna aminovalerica	77.8004	177	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.17	99.14	0.90	0.89	3	-
GCF_900142215.1	s__Anaerocolumna jejuensis	77.6012	213	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143645.1	s__Anaerocolumna xylanovorans	77.4702	193	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142955.1	s__Anaerosporobacter mobilis	77.4345	79	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218355.1	s__Anaerocolumna sp014218355	77.429	204	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655565.1	s__Anaerocolumna sp015655565	77.2723	111	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752155.1	s__Mobilisporobacter senegalensis	77.2231	98	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655075.1	s__Anaerocolumna sp015655075	77.0622	154	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016591975.1	s__TB5 sp016591975	77.0217	110	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TB5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002419585.1	s__Velocimicrobium sp002419585	76.9666	74	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Velocimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012839085.1	s__Mobilitalea sp012839085	76.4928	58	1748	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:53,788] [INFO] GTDB search result was written to GCF_014202875.1_ASM1420287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:53,788] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:53,791] [INFO] DFAST_QC result json was written to GCF_014202875.1_ASM1420287v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:53,791] [INFO] DFAST_QC completed!
[2024-01-24 13:38:53,791] [INFO] Total running time: 0h1m12s