[2024-01-24 12:53:56,380] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:56,387] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:56,387] [INFO] DQC Reference Directory: /var/lib/cwl/stg3172eb39-4f49-4045-b24b-8359433d1b6e/dqc_reference
[2024-01-24 12:53:57,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:57,746] [INFO] Task started: Prodigal
[2024-01-24 12:53:57,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg417d0c53-ea2f-4562-8991-e3c2948ec3db/GCF_004346095.1_ASM434609v1_genomic.fna.gz | prodigal -d GCF_004346095.1_ASM434609v1_genomic.fna/cds.fna -a GCF_004346095.1_ASM434609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:05,145] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:05,145] [INFO] Task started: HMMsearch
[2024-01-24 12:54:05,145] [INFO] Running command: hmmsearch --tblout GCF_004346095.1_ASM434609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3172eb39-4f49-4045-b24b-8359433d1b6e/dqc_reference/reference_markers.hmm GCF_004346095.1_ASM434609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:05,411] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:05,412] [INFO] Found 6/6 markers.
[2024-01-24 12:54:05,442] [INFO] Query marker FASTA was written to GCF_004346095.1_ASM434609v1_genomic.fna/markers.fasta
[2024-01-24 12:54:05,443] [INFO] Task started: Blastn
[2024-01-24 12:54:05,443] [INFO] Running command: blastn -query GCF_004346095.1_ASM434609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3172eb39-4f49-4045-b24b-8359433d1b6e/dqc_reference/reference_markers.fasta -out GCF_004346095.1_ASM434609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:06,094] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:06,097] [INFO] Selected 16 target genomes.
[2024-01-24 12:54:06,098] [INFO] Target genome list was writen to GCF_004346095.1_ASM434609v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:06,105] [INFO] Task started: fastANI
[2024-01-24 12:54:06,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg417d0c53-ea2f-4562-8991-e3c2948ec3db/GCF_004346095.1_ASM434609v1_genomic.fna.gz --refList GCF_004346095.1_ASM434609v1_genomic.fna/target_genomes.txt --output GCF_004346095.1_ASM434609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:15,108] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:15,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3172eb39-4f49-4045-b24b-8359433d1b6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:15,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3172eb39-4f49-4045-b24b-8359433d1b6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:15,121] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:54:15,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:15,122] [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
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	100.0	983	990	95	conclusive
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	99.9991	990	990	95	conclusive
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	81.5496	100	990	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	79.5594	189	990	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	79.355	143	990	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	78.7411	66	990	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	78.4545	108	990	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	78.4219	129	990	95	below_threshold
Hespellia stercorisuis	strain=DSM 15480	GCA_900142165.1	180311	180311	type	True	78.2546	101	990	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	78.1778	167	990	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.8655	111	990	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.5812	111	990	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.4978	59	990	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.2924	95	990	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	77.1797	99	990	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.1386	124	990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:15,123] [INFO] DFAST Taxonomy check result was written to GCF_004346095.1_ASM434609v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:15,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:15,124] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:15,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3172eb39-4f49-4045-b24b-8359433d1b6e/dqc_reference/checkm_data
[2024-01-24 12:54:15,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:15,157] [INFO] Task started: CheckM
[2024-01-24 12:54:15,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004346095.1_ASM434609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004346095.1_ASM434609v1_genomic.fna/checkm_input GCF_004346095.1_ASM434609v1_genomic.fna/checkm_result
[2024-01-24 12:54:43,930] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:43,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:43,952] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:43,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:43,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004346095.1_ASM434609v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:43,953] [INFO] Task started: Blastn
[2024-01-24 12:54:43,953] [INFO] Running command: blastn -query GCF_004346095.1_ASM434609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3172eb39-4f49-4045-b24b-8359433d1b6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004346095.1_ASM434609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:45,013] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:45,017] [INFO] Selected 19 target genomes.
[2024-01-24 12:54:45,017] [INFO] Target genome list was writen to GCF_004346095.1_ASM434609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:45,049] [INFO] Task started: fastANI
[2024-01-24 12:54:45,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg417d0c53-ea2f-4562-8991-e3c2948ec3db/GCF_004346095.1_ASM434609v1_genomic.fna.gz --refList GCF_004346095.1_ASM434609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004346095.1_ASM434609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:54,724] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:54,738] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:54,739] [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_004346095.1	s__Faecalimonas umbilicata	100.0	983	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.30	97.78	0.83	0.78	20	conclusive
GCA_900546325.1	s__Faecalimonas sp900546325	87.5263	632	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	99.83	99.66	0.93	0.88	3	-
GCF_003435815.1	s__CAG-317 sp000433215	79.8152	145	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCF_900104635.1	s__Faecalimonas phoceensis	79.5858	188	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.10	95.01	0.81	0.60	21	-
GCA_902381685.1	s__Faecalimonas sp000209385	79.4602	151	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	99.49	98.98	0.93	0.86	3	-
GCF_018228665.1	s__UBA9414 sp003458885	79.3654	176	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	97.84	97.84	0.85	0.85	3	-
GCA_900550235.1	s__Faecalimonas sp900550235	79.3	135	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000155875.1	s__Bariatricus comes	78.8795	133	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCA_900551895.1	s__Faecalimonas sp900551895	78.662	121	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.69	98.58	0.83	0.80	3	-
GCF_013300725.1	s__Bariatricus comes_A	78.484	132	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCA_018365895.1	s__UBA9414 sp018365895	78.1314	144	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433535.1	s__CAG-317 sp000433535	77.7007	117	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.49	98.19	0.84	0.83	3	-
GCF_012524165.2	s__Muricomes sp012524165	77.5812	111	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576335.1	s__UBA7109 sp910576335	77.5066	75	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	99.46	98.92	0.97	0.94	3	-
GCA_900550865.1	s__Dorea_A sp900550865	77.2022	104	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556835.1	s__Faecalimonas sp900556835	77.0522	113	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904419285.1	s__Mediterraneibacter caccogallinarum	76.885	61	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.44	97.89	0.90	0.83	10	-
GCA_016295505.1	s__Dorea_A sp016295505	76.8671	84	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120075.1	s__Mediterraneibacter excrementigallinarum_A	76.5558	67	990	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.40	96.45	0.78	0.77	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:54,740] [INFO] GTDB search result was written to GCF_004346095.1_ASM434609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:54,741] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:54,745] [INFO] DFAST_QC result json was written to GCF_004346095.1_ASM434609v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:54,745] [INFO] DFAST_QC completed!
[2024-01-24 12:54:54,745] [INFO] Total running time: 0h0m58s