[2024-01-24 13:36:45,584] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg19b1f8e4-337a-4d5c-b1ae-2e18c95eb8ad/dqc_reference
[2024-01-24 13:36:46,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,856] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,856] [INFO] Running command: gunzip -c /var/lib/cwl/stg22e4b3b1-5795-4c38-8e4b-420d14b34809/GCF_014287475.1_ASM1428747v1_genomic.fna.gz | prodigal -d GCF_014287475.1_ASM1428747v1_genomic.fna/cds.fna -a GCF_014287475.1_ASM1428747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:55,445] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:55,446] [INFO] Task started: HMMsearch
[2024-01-24 13:36:55,446] [INFO] Running command: hmmsearch --tblout GCF_014287475.1_ASM1428747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19b1f8e4-337a-4d5c-b1ae-2e18c95eb8ad/dqc_reference/reference_markers.hmm GCF_014287475.1_ASM1428747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:55,740] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:55,742] [INFO] Found 6/6 markers.
[2024-01-24 13:36:55,778] [INFO] Query marker FASTA was written to GCF_014287475.1_ASM1428747v1_genomic.fna/markers.fasta
[2024-01-24 13:36:55,779] [INFO] Task started: Blastn
[2024-01-24 13:36:55,779] [INFO] Running command: blastn -query GCF_014287475.1_ASM1428747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19b1f8e4-337a-4d5c-b1ae-2e18c95eb8ad/dqc_reference/reference_markers.fasta -out GCF_014287475.1_ASM1428747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:56,466] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:56,471] [INFO] Selected 21 target genomes.
[2024-01-24 13:36:56,471] [INFO] Target genome list was writen to GCF_014287475.1_ASM1428747v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:56,500] [INFO] Task started: fastANI
[2024-01-24 13:36:56,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg22e4b3b1-5795-4c38-8e4b-420d14b34809/GCF_014287475.1_ASM1428747v1_genomic.fna.gz --refList GCF_014287475.1_ASM1428747v1_genomic.fna/target_genomes.txt --output GCF_014287475.1_ASM1428747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:07,272] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:07,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19b1f8e4-337a-4d5c-b1ae-2e18c95eb8ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:07,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19b1f8e4-337a-4d5c-b1ae-2e18c95eb8ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:07,285] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:07,286] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:07,286] [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
Mediterraneibacter massiliensis	strain=Marseille-P2086	GCA_001487105.1	1720300	1720300	type	True	79.9766	494	1196	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.9231	191	1196	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.8705	190	1196	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.8692	182	1196	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.8297	191	1196	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	77.8082	141	1196	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	77.6244	130	1196	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	77.5872	85	1196	95	below_threshold
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	77.5529	73	1196	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.5484	133	1196	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	77.4306	103	1196	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	77.2884	87	1196	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	77.2671	90	1196	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.0935	88	1196	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:07,287] [INFO] DFAST Taxonomy check result was written to GCF_014287475.1_ASM1428747v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:07,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:07,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:07,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19b1f8e4-337a-4d5c-b1ae-2e18c95eb8ad/dqc_reference/checkm_data
[2024-01-24 13:37:07,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:07,328] [INFO] Task started: CheckM
[2024-01-24 13:37:07,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287475.1_ASM1428747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287475.1_ASM1428747v1_genomic.fna/checkm_input GCF_014287475.1_ASM1428747v1_genomic.fna/checkm_result
[2024-01-24 13:37:39,471] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:39,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:39,490] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:39,491] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:39,491] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287475.1_ASM1428747v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:39,492] [INFO] Task started: Blastn
[2024-01-24 13:37:39,492] [INFO] Running command: blastn -query GCF_014287475.1_ASM1428747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19b1f8e4-337a-4d5c-b1ae-2e18c95eb8ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287475.1_ASM1428747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:40,589] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:40,593] [INFO] Selected 21 target genomes.
[2024-01-24 13:37:40,593] [INFO] Target genome list was writen to GCF_014287475.1_ASM1428747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:40,617] [INFO] Task started: fastANI
[2024-01-24 13:37:40,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg22e4b3b1-5795-4c38-8e4b-420d14b34809/GCF_014287475.1_ASM1428747v1_genomic.fna.gz --refList GCF_014287475.1_ASM1428747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287475.1_ASM1428747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:53,597] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:53,617] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:53,617] [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_014287475.1	s__Mediterraneibacter sp014287475	100.0	1196	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.03	96.03	0.75	0.75	2	conclusive
GCF_001487105.1	s__Mediterraneibacter massiliensis	79.9664	494	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.29	98.08	0.94	0.85	4	-
GCA_900541505.1	s__Mediterraneibacter sp900541505	78.6623	378	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.61	98.61	0.89	0.89	2	-
GCF_008121495.1	s__Ruminococcus_B gnavus	77.859	190	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	98.58	96.13	0.80	0.66	102	-
GCF_013300725.1	s__Bariatricus comes_A	77.8043	81	1196	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_900765975.1	s__Schaedlerella sp900765975	77.8031	123	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.94	99.94	0.80	0.80	2	-
GCF_003149105.1	s__Muricomes contortus_C	77.7193	172	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000155205.1	s__Mediterraneibacter lactaris	77.6551	128	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCA_013911065.1	s__Muricomes sp013911065	77.6464	157	1196	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_000155875.1	s__Bariatricus comes	77.5638	79	1196	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_000403295.2	s__Schaedlerella sp000403295	77.422	114	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.10	98.10	0.85	0.85	2	-
GCA_910574195.1	s__Schaedlerella sp910574195	77.2988	127	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.97	99.97	0.98	0.98	2	-
GCA_900544395.1	s__Ruminococcus_B sp900544395	77.2522	180	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	99.21	99.21	0.88	0.88	2	-
GCF_004346095.1	s__Faecalimonas umbilicata	77.103	86	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.30	97.78	0.83	0.78	20	-
GCA_900751785.1	s__Mediterraneibacter faecigallinarum	76.9358	130	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.56	97.84	0.86	0.78	4	-
GCA_019112765.1	s__Mediterraneibacter norwichensis	76.8502	134	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.85	97.86	0.81	0.76	3	-
GCA_019119745.1	s__Mediterraneibacter gallistercoris	76.7953	97	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905209865.1	s__Mediterraneibacter sp900752395	76.7518	122	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.94	99.94	0.94	0.94	2	-
GCA_900553885.1	s__Mediterraneibacter sp900553885	76.7373	146	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016295505.1	s__Dorea_A sp016295505	76.597	57	1196	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	75.2618	56	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:53,620] [INFO] GTDB search result was written to GCF_014287475.1_ASM1428747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:53,620] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:53,624] [INFO] DFAST_QC result json was written to GCF_014287475.1_ASM1428747v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:53,625] [INFO] DFAST_QC completed!
[2024-01-24 13:37:53,625] [INFO] Total running time: 0h1m8s