[2023-06-28 17:35:52,538] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:35:52,542] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:35:52,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg211007ca-0a38-42a5-ba4c-764f65f76a82/dqc_reference
[2023-06-28 17:35:53,875] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:35:53,876] [INFO] Task started: Prodigal
[2023-06-28 17:35:53,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg5012aef8-c3a9-4c20-a306-49c3765106e3/GCA_019411455.1_ASM1941145v1_genomic.fna.gz | prodigal -d GCA_019411455.1_ASM1941145v1_genomic.fna/cds.fna -a GCA_019411455.1_ASM1941145v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:35:59,936] [INFO] Task succeeded: Prodigal
[2023-06-28 17:35:59,937] [INFO] Task started: HMMsearch
[2023-06-28 17:35:59,937] [INFO] Running command: hmmsearch --tblout GCA_019411455.1_ASM1941145v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg211007ca-0a38-42a5-ba4c-764f65f76a82/dqc_reference/reference_markers.hmm GCA_019411455.1_ASM1941145v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:36:00,206] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:36:00,209] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5012aef8-c3a9-4c20-a306-49c3765106e3/GCA_019411455.1_ASM1941145v1_genomic.fna.gz]
[2023-06-28 17:36:00,248] [INFO] Query marker FASTA was written to GCA_019411455.1_ASM1941145v1_genomic.fna/markers.fasta
[2023-06-28 17:36:00,248] [INFO] Task started: Blastn
[2023-06-28 17:36:00,248] [INFO] Running command: blastn -query GCA_019411455.1_ASM1941145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg211007ca-0a38-42a5-ba4c-764f65f76a82/dqc_reference/reference_markers.fasta -out GCA_019411455.1_ASM1941145v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:36:00,933] [INFO] Task succeeded: Blastn
[2023-06-28 17:36:00,942] [INFO] Selected 22 target genomes.
[2023-06-28 17:36:00,943] [INFO] Target genome list was writen to GCA_019411455.1_ASM1941145v1_genomic.fna/target_genomes.txt
[2023-06-28 17:36:00,945] [INFO] Task started: fastANI
[2023-06-28 17:36:00,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg5012aef8-c3a9-4c20-a306-49c3765106e3/GCA_019411455.1_ASM1941145v1_genomic.fna.gz --refList GCA_019411455.1_ASM1941145v1_genomic.fna/target_genomes.txt --output GCA_019411455.1_ASM1941145v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:36:14,548] [INFO] Task succeeded: fastANI
[2023-06-28 17:36:14,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg211007ca-0a38-42a5-ba4c-764f65f76a82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:36:14,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg211007ca-0a38-42a5-ba4c-764f65f76a82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:36:14,560] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 17:36:14,560] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 17:36:14,560] [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
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	97.6561	549	703	95	conclusive
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	80.556	225	703	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	80.5304	224	703	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	80.4571	222	703	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	79.3946	84	703	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	79.0404	165	703	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	78.6486	65	703	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	78.1062	147	703	95	below_threshold
Agathobacter ruminis	strain=JK623	GCA_002735305.1	1712665	1712665	type	True	77.5024	52	703	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	77.113	56	703	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	76.9113	79	703	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:36:14,563] [INFO] DFAST Taxonomy check result was written to GCA_019411455.1_ASM1941145v1_genomic.fna/tc_result.tsv
[2023-06-28 17:36:14,564] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:36:14,564] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:36:14,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg211007ca-0a38-42a5-ba4c-764f65f76a82/dqc_reference/checkm_data
[2023-06-28 17:36:14,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:36:14,600] [INFO] Task started: CheckM
[2023-06-28 17:36:14,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019411455.1_ASM1941145v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019411455.1_ASM1941145v1_genomic.fna/checkm_input GCA_019411455.1_ASM1941145v1_genomic.fna/checkm_result
[2023-06-28 17:36:39,925] [INFO] Task succeeded: CheckM
[2023-06-28 17:36:39,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:36:39,951] [INFO] ===== Completeness check finished =====
[2023-06-28 17:36:39,952] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:36:39,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019411455.1_ASM1941145v1_genomic.fna/markers.fasta)
[2023-06-28 17:36:39,952] [INFO] Task started: Blastn
[2023-06-28 17:36:39,953] [INFO] Running command: blastn -query GCA_019411455.1_ASM1941145v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg211007ca-0a38-42a5-ba4c-764f65f76a82/dqc_reference/reference_markers_gtdb.fasta -out GCA_019411455.1_ASM1941145v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:36:40,991] [INFO] Task succeeded: Blastn
[2023-06-28 17:36:40,996] [INFO] Selected 15 target genomes.
[2023-06-28 17:36:40,996] [INFO] Target genome list was writen to GCA_019411455.1_ASM1941145v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:36:40,998] [INFO] Task started: fastANI
[2023-06-28 17:36:40,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg5012aef8-c3a9-4c20-a306-49c3765106e3/GCA_019411455.1_ASM1941145v1_genomic.fna.gz --refList GCA_019411455.1_ASM1941145v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019411455.1_ASM1941145v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:36:48,823] [INFO] Task succeeded: fastANI
[2023-06-28 17:36:48,839] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:36:48,839] [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_000174195.1	s__Roseburia inulinivorans	97.6561	549	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	conclusive
GCA_900542495.1	s__Roseburia sp900542495	89.3798	479	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.47	97.09	0.82	0.76	4	-
GCF_900537995.1	s__Roseburia intestinalis	80.5036	225	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	-
GCA_900756925.1	s__Roseburia sp900756925	79.9496	153	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.83	98.83	0.90	0.90	2	-
GCA_003483745.1	s__Roseburia sp003483745	79.319	207	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCA_900550935.1	s__Roseburia sp900550935	79.1067	171	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.33	98.19	0.83	0.82	3	-
GCF_001940165.1	s__Roseburia sp001940165	79.0777	177	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225345.1	s__Roseburia hominis	79.0264	166	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCF_003470905.1	s__Roseburia sp003470905	78.9736	223	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCA_902363825.1	s__CAG-45 sp000438375	78.2439	118	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	98.60	98.28	0.92	0.87	6	-
GCF_002735305.1	s__Agathobacter ruminis	77.5024	52	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.23	97.94	0.91	0.87	3	-
GCA_900552085.1	s__Agathobacter sp900552085	77.4275	71	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCA_014804775.1	s__Roseburia sp014804775	76.9851	90	703	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:36:48,841] [INFO] GTDB search result was written to GCA_019411455.1_ASM1941145v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:36:48,841] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:36:48,845] [INFO] DFAST_QC result json was written to GCA_019411455.1_ASM1941145v1_genomic.fna/dqc_result.json
[2023-06-28 17:36:48,845] [INFO] DFAST_QC completed!
[2023-06-28 17:36:48,845] [INFO] Total running time: 0h0m56s