[2024-01-24 12:06:50,817] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:50,819] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:50,819] [INFO] DQC Reference Directory: /var/lib/cwl/stg8644c7d2-afeb-44af-960f-076f9c969380/dqc_reference
[2024-01-24 12:06:52,019] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:52,020] [INFO] Task started: Prodigal
[2024-01-24 12:06:52,020] [INFO] Running command: gunzip -c /var/lib/cwl/stge22a2efc-b292-4b2c-a885-0398d81608da/GCF_016595795.1_ASM1659579v1_genomic.fna.gz | prodigal -d GCF_016595795.1_ASM1659579v1_genomic.fna/cds.fna -a GCF_016595795.1_ASM1659579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:01,024] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:01,025] [INFO] Task started: HMMsearch
[2024-01-24 12:07:01,025] [INFO] Running command: hmmsearch --tblout GCF_016595795.1_ASM1659579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8644c7d2-afeb-44af-960f-076f9c969380/dqc_reference/reference_markers.hmm GCF_016595795.1_ASM1659579v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:01,368] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:01,369] [INFO] Found 6/6 markers.
[2024-01-24 12:07:01,416] [INFO] Query marker FASTA was written to GCF_016595795.1_ASM1659579v1_genomic.fna/markers.fasta
[2024-01-24 12:07:01,416] [INFO] Task started: Blastn
[2024-01-24 12:07:01,417] [INFO] Running command: blastn -query GCF_016595795.1_ASM1659579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8644c7d2-afeb-44af-960f-076f9c969380/dqc_reference/reference_markers.fasta -out GCF_016595795.1_ASM1659579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:02,006] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:02,009] [INFO] Selected 23 target genomes.
[2024-01-24 12:07:02,010] [INFO] Target genome list was writen to GCF_016595795.1_ASM1659579v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:02,018] [INFO] Task started: fastANI
[2024-01-24 12:07:02,018] [INFO] Running command: fastANI --query /var/lib/cwl/stge22a2efc-b292-4b2c-a885-0398d81608da/GCF_016595795.1_ASM1659579v1_genomic.fna.gz --refList GCF_016595795.1_ASM1659579v1_genomic.fna/target_genomes.txt --output GCF_016595795.1_ASM1659579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:18,392] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:18,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8644c7d2-afeb-44af-960f-076f9c969380/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:18,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8644c7d2-afeb-44af-960f-076f9c969380/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:18,413] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:18,413] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:18,414] [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 fungisolvens	strain=TW1	GCA_014193895.1	1604897	1604897	type	True	89.0085	1355	1873	95	below_threshold
Clostridium zeae	strain=CSC2	GCA_017312485.1	2759022	2759022	type	True	88.8899	1455	1873	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	80.8712	852	1873	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	77.6994	222	1873	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	77.3035	214	1873	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	77.2586	208	1873	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	77.0932	160	1873	95	below_threshold
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	77.0357	176	1873	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	76.8501	192	1873	95	below_threshold
Clostridium amylolyticum	strain=DSM 21864	GCA_900142075.1	1121298	1121298	type	True	76.7645	144	1873	95	below_threshold
Clostridium vincentii	strain=DSM 10228	GCA_002995745.1	52704	52704	type	True	76.7516	126	1873	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	76.7044	187	1873	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	76.6919	277	1873	95	below_threshold
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	76.5497	103	1873	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.2496	133	1873	95	below_threshold
Clostridium lacusfryxellense	strain=DSM 14205	GCA_018861735.1	205328	205328	type	True	76.1146	143	1873	95	below_threshold
Clostridium frigoris	strain=DSM 14204	GCA_018861865.1	205327	205327	type	True	76.0517	93	1873	95	below_threshold
Romboutsia ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	75.417	69	1873	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	74.8273	68	1873	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:18,415] [INFO] DFAST Taxonomy check result was written to GCF_016595795.1_ASM1659579v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:18,416] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:18,416] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:18,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8644c7d2-afeb-44af-960f-076f9c969380/dqc_reference/checkm_data
[2024-01-24 12:07:18,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:18,477] [INFO] Task started: CheckM
[2024-01-24 12:07:18,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016595795.1_ASM1659579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016595795.1_ASM1659579v1_genomic.fna/checkm_input GCF_016595795.1_ASM1659579v1_genomic.fna/checkm_result
[2024-01-24 12:07:50,592] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:50,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:50,621] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:50,622] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:50,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016595795.1_ASM1659579v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:50,623] [INFO] Task started: Blastn
[2024-01-24 12:07:50,623] [INFO] Running command: blastn -query GCF_016595795.1_ASM1659579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8644c7d2-afeb-44af-960f-076f9c969380/dqc_reference/reference_markers_gtdb.fasta -out GCF_016595795.1_ASM1659579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:51,413] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:51,417] [INFO] Selected 9 target genomes.
[2024-01-24 12:07:51,417] [INFO] Target genome list was writen to GCF_016595795.1_ASM1659579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:51,425] [INFO] Task started: fastANI
[2024-01-24 12:07:51,425] [INFO] Running command: fastANI --query /var/lib/cwl/stge22a2efc-b292-4b2c-a885-0398d81608da/GCF_016595795.1_ASM1659579v1_genomic.fna.gz --refList GCF_016595795.1_ASM1659579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016595795.1_ASM1659579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:01,490] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:01,506] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:01,506] [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_016595795.1	s__Clostridium_AR sp016595795	100.0	1871	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014193895.1	s__Clostridium_AR fungisolvens	88.9915	1357	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017312485.1	s__Clostridium_AR sp017312485	88.8797	1456	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004015185.1	s__Clostridium_AR sp004015185	80.8765	851	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009928445.1	s__Clostridium_AR sp009928445	80.8627	852	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018372875.1	s__Clostridium sp018372875	76.7844	173	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.91	98.91	0.87	0.87	2	-
GCA_018336475.1	s__Romboutsia sp018336475	75.5462	74	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900015215.1	s__Romboutsia ilealis	75.4232	69	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.59	98.59	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:01,508] [INFO] GTDB search result was written to GCF_016595795.1_ASM1659579v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:01,509] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:01,514] [INFO] DFAST_QC result json was written to GCF_016595795.1_ASM1659579v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:01,515] [INFO] DFAST_QC completed!
[2024-01-24 12:08:01,515] [INFO] Total running time: 0h1m11s