[2024-01-24 13:41:10,329] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,331] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,331] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2e75f85-9a48-4b83-b689-a8d302911e69/dqc_reference
[2024-01-24 13:41:11,603] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,604] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,604] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bac1c35-0128-4ca1-8c93-7b2628ac76ee/GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/cds.fna -a GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:16,892] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:16,892] [INFO] Task started: HMMsearch
[2024-01-24 13:41:16,892] [INFO] Running command: hmmsearch --tblout GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2e75f85-9a48-4b83-b689-a8d302911e69/dqc_reference/reference_markers.hmm GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:17,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:17,200] [INFO] Found 6/6 markers.
[2024-01-24 13:41:17,229] [INFO] Query marker FASTA was written to GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:41:17,230] [INFO] Task started: Blastn
[2024-01-24 13:41:17,230] [INFO] Running command: blastn -query GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2e75f85-9a48-4b83-b689-a8d302911e69/dqc_reference/reference_markers.fasta -out GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:17,860] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:17,862] [INFO] Selected 27 target genomes.
[2024-01-24 13:41:17,863] [INFO] Target genome list was writen to GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:41:17,871] [INFO] Task started: fastANI
[2024-01-24 13:41:17,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bac1c35-0128-4ca1-8c93-7b2628ac76ee/GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna.gz --refList GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:34,099] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:34,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2e75f85-9a48-4b83-b689-a8d302911e69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:34,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2e75f85-9a48-4b83-b689-a8d302911e69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:34,121] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:34,122] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:34,122] [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 collagenovorans	strain=DSM 3089	GCA_900130005.1	29357	29357	type	True	100.0	1143	1145	95	conclusive
Hathewaya histolytica	strain=NCTC503	GCA_901482605.1	1498	1498	type	True	76.8702	165	1145	95	below_threshold
Hathewaya massiliensis	strain=Marseille-P3545	GCA_902143515.1	1964382	1964382	type	True	76.7591	192	1145	95	below_threshold
Clostridium ihumii	strain=AP5	GCA_000612845.1	1470356	1470356	type	True	76.6864	227	1145	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	76.3644	154	1145	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.3565	166	1145	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.3087	157	1145	95	below_threshold
Clostridium thermopalmarium	strain=DSM 5974	GCA_002995795.1	29373	29373	suspected-type	True	76.1597	80	1145	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.1552	139	1145	95	below_threshold
Clostridium thermopalmarium	strain=DSM 5974	GCA_003097175.1	29373	29373	suspected-type	True	76.1274	85	1145	95	below_threshold
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	76.1127	108	1145	95	below_threshold
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	76.0783	120	1145	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	76.0629	121	1145	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.0627	131	1145	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	76.0574	108	1145	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	76.0467	156	1145	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	75.9936	164	1145	95	below_threshold
Clostridium aciditolerans	strain=DSM 17425	GCA_016316925.1	339861	339861	type	True	75.9854	115	1145	95	below_threshold
Clostridium putrefaciens	strain=NCTC9836	GCA_900461105.1	99675	99675	type	True	75.9488	82	1145	95	below_threshold
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	75.9137	141	1145	95	below_threshold
Clostridium acidisoli	strain=DSM 12555	GCA_900176305.1	91624	91624	type	True	75.8944	108	1145	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	75.8814	148	1145	95	below_threshold
Clostridium pascui	strain=DSM 10365	GCA_016908015.1	46609	46609	type	True	75.869	123	1145	95	below_threshold
Clostridium akagii	strain=DSM 12554	GCA_000686725.1	91623	91623	type	True	75.8663	90	1145	95	below_threshold
Clostridium gasigenes	strain=DSM 12272	GCA_900104115.1	94869	94869	type	True	75.8425	126	1145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:34,123] [INFO] DFAST Taxonomy check result was written to GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:34,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:34,124] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:34,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2e75f85-9a48-4b83-b689-a8d302911e69/dqc_reference/checkm_data
[2024-01-24 13:41:34,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:34,161] [INFO] Task started: CheckM
[2024-01-24 13:41:34,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/checkm_input GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:41:58,634] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:58,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:58,658] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:58,658] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:58,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:41:58,659] [INFO] Task started: Blastn
[2024-01-24 13:41:58,660] [INFO] Running command: blastn -query GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2e75f85-9a48-4b83-b689-a8d302911e69/dqc_reference/reference_markers_gtdb.fasta -out GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:59,438] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:59,442] [INFO] Selected 26 target genomes.
[2024-01-24 13:41:59,442] [INFO] Target genome list was writen to GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:59,476] [INFO] Task started: fastANI
[2024-01-24 13:41:59,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bac1c35-0128-4ca1-8c93-7b2628ac76ee/GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna.gz --refList GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:14,808] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:14,833] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:14,834] [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_900130005.1	s__Clostridium_D collagenovorans	100.0	1143	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003288255.1	s__Hathewaya sp003288255	77.9352	195	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000821305.1	s__Clostridium_J sp000821305	76.9077	144	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	100.00	100.00	1.00	1.00	3	-
GCF_901482605.1	s__Hathewaya histolytica	76.8827	166	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003606265.1	s__Clostridium septicum	76.8038	140	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	-
GCF_902143515.1	s__Hathewaya massiliensis	76.7464	192	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002008345.1	s__Clostridium_F tepidum	76.7339	149	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
GCF_000612845.1	s__Clostridium_J ihumii	76.697	225	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900129365.1	s__Clostridium_AH fallax	76.3285	157	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000285575.1	s__Clostridium_J senegalense	76.2787	176	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	97.19	95.52	0.93	0.91	5	-
GCA_002455975.1	s__Clostridium_J sp002455975	76.1889	154	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002995795.1	s__Clostridium_H thermopalmarium	76.1597	80	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	99.57	99.32	0.95	0.92	4	-
GCF_003614235.1	s__Clostridium_H haemolyticum	76.1152	127	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.44	97.38	0.90	0.84	13	-
GCF_900176615.1	s__Clostridium_H massiliodielmoense	76.1149	108	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.64	96.44	0.92	0.87	5	-
GCF_000789395.1	s__Clostridium baratii	76.0858	133	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.53	95.37	0.92	0.89	15	-
GCF_000014125.1	s__Clostridium_H novyi	76.0845	129	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.92	96.35	0.94	0.92	7	-
GCA_002381695.1	s__Clostridium_J sp002381695	76.0513	159	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295725.1	s__Clostridium_P tarantellae	76.0482	156	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889325.1	s__Clostridium_F botulinum_A	75.9774	153	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	95.92	95.51	0.89	0.85	52	-
GCF_900091705.1	s__Clostridium_P mediterraneense	75.9347	139	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900461105.1	s__Clostridium_L putrefaciens	75.9252	82	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176305.1	s__Clostridium_I acidisoli	75.9214	109	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001623875.1	s__Clostridium_AM magnum	75.9137	125	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.97	0.98	0.98	2	-
GCF_014836325.1	s__Clostridium sp014836325	75.8814	148	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908015.1	s__Clostridium_AK pascui	75.869	123	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686725.1	s__Clostridium_I akagii	75.8498	91	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:14,840] [INFO] GTDB search result was written to GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:14,840] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:14,846] [INFO] DFAST_QC result json was written to GCF_900130005.1_IMG-taxon_2585428078_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:42:14,847] [INFO] DFAST_QC completed!
[2024-01-24 13:42:14,847] [INFO] Total running time: 0h1m5s