[2024-01-24 10:47:40,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f632f14-668c-4932-a1a7-5324b554f922/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe782858-a732-41a5-ae1d-ecd69d5d55fa/GCF_000484505.2_ASM48450v2_genomic.fna.gz | prodigal -d GCF_000484505.2_ASM48450v2_genomic.fna/cds.fna -a GCF_000484505.2_ASM48450v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:52,406] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:52,406] [INFO] Task started: HMMsearch
[2024-01-24 10:47:52,406] [INFO] Running command: hmmsearch --tblout GCF_000484505.2_ASM48450v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f632f14-668c-4932-a1a7-5324b554f922/dqc_reference/reference_markers.hmm GCF_000484505.2_ASM48450v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:52,712] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:52,713] [INFO] Found 6/6 markers.
[2024-01-24 10:47:52,752] [INFO] Query marker FASTA was written to GCF_000484505.2_ASM48450v2_genomic.fna/markers.fasta
[2024-01-24 10:47:52,753] [INFO] Task started: Blastn
[2024-01-24 10:47:52,753] [INFO] Running command: blastn -query GCF_000484505.2_ASM48450v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f632f14-668c-4932-a1a7-5324b554f922/dqc_reference/reference_markers.fasta -out GCF_000484505.2_ASM48450v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:53,342] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:53,346] [INFO] Selected 11 target genomes.
[2024-01-24 10:47:53,346] [INFO] Target genome list was writen to GCF_000484505.2_ASM48450v2_genomic.fna/target_genomes.txt
[2024-01-24 10:47:53,354] [INFO] Task started: fastANI
[2024-01-24 10:47:53,354] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe782858-a732-41a5-ae1d-ecd69d5d55fa/GCF_000484505.2_ASM48450v2_genomic.fna.gz --refList GCF_000484505.2_ASM48450v2_genomic.fna/target_genomes.txt --output GCF_000484505.2_ASM48450v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:07,208] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:07,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f632f14-668c-4932-a1a7-5324b554f922/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:07,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f632f14-668c-4932-a1a7-5324b554f922/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:07,218] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 10:48:07,219] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:48:07,219] [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
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	100.0	1451	1451	95	inconclusive
Clostridium autoethanogenum	strain=DSM 10061	GCA_001484725.1	84023	84023	suspected-type	True	99.9953	1449	1451	95	inconclusive
Clostridium autoethanogenum	strain=JA1-1	GCA_002189005.1	84023	84023	suspected-type	True	99.9746	1427	1451	95	inconclusive
Clostridium autoethanogenum	strain=DSM 10061	GCA_000427255.1	84023	84023	suspected-type	True	99.9584	1382	1451	95	inconclusive
Clostridium ljungdahlii	strain=DSM 13528	GCA_000143685.1	1538	1538	suspected-type	True	99.056	1348	1451	95	inconclusive
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	79.3751	436	1451	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	78.815	422	1451	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	78.8115	417	1451	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	77.9839	353	1451	95	below_threshold
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	76.8068	70	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:07,221] [INFO] DFAST Taxonomy check result was written to GCF_000484505.2_ASM48450v2_genomic.fna/tc_result.tsv
[2024-01-24 10:48:07,221] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:07,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:07,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f632f14-668c-4932-a1a7-5324b554f922/dqc_reference/checkm_data
[2024-01-24 10:48:07,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:07,271] [INFO] Task started: CheckM
[2024-01-24 10:48:07,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000484505.2_ASM48450v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000484505.2_ASM48450v2_genomic.fna/checkm_input GCF_000484505.2_ASM48450v2_genomic.fna/checkm_result
[2024-01-24 10:48:35,504] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:35,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:35,527] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:35,527] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:35,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000484505.2_ASM48450v2_genomic.fna/markers.fasta)
[2024-01-24 10:48:35,528] [INFO] Task started: Blastn
[2024-01-24 10:48:35,528] [INFO] Running command: blastn -query GCF_000484505.2_ASM48450v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f632f14-668c-4932-a1a7-5324b554f922/dqc_reference/reference_markers_gtdb.fasta -out GCF_000484505.2_ASM48450v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:36,292] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:36,294] [INFO] Selected 9 target genomes.
[2024-01-24 10:48:36,295] [INFO] Target genome list was writen to GCF_000484505.2_ASM48450v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:36,301] [INFO] Task started: fastANI
[2024-01-24 10:48:36,301] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe782858-a732-41a5-ae1d-ecd69d5d55fa/GCF_000484505.2_ASM48450v2_genomic.fna.gz --refList GCF_000484505.2_ASM48450v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000484505.2_ASM48450v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:47,587] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:47,601] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:47,601] [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_000143685.1	s__Clostridium_B ljungdahlii	99.0395	1349	1451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.76	97.79	0.92	0.88	9	conclusive
GCF_001675165.1	s__Clostridium_B ragsdalei	94.7719	1174	1451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.18	98.18	0.88	0.88	2	-
GCF_001636845.1	s__Clostridium_B ljungdahlii_A	94.3102	1118	1451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006395.2	s__Clostridium_B sp004006395	93.9874	1190	1451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633595.2	s__Clostridium_AM drakei	79.4289	496	1451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	100.00	100.00	1.00	1.00	2	-
GCF_017874415.1	s__Clostridium_B algifaecis	78.8707	345	1451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016505.1	s__Clostridium_B kluyveri	78.8066	423	1451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	97.52	95.05	0.91	0.81	3	-
GCF_002995845.1	s__Clostridium_B luticellarii	78.3706	364	1451	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:47,603] [INFO] GTDB search result was written to GCF_000484505.2_ASM48450v2_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:47,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:47,610] [INFO] DFAST_QC result json was written to GCF_000484505.2_ASM48450v2_genomic.fna/dqc_result.json
[2024-01-24 10:48:47,610] [INFO] DFAST_QC completed!
[2024-01-24 10:48:47,610] [INFO] Total running time: 0h1m7s