[2024-01-25 20:22:35,336] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:35,337] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:35,337] [INFO] DQC Reference Directory: /var/lib/cwl/stg24971c5b-dc73-4d0b-8fd6-377558fe5dfe/dqc_reference
[2024-01-25 20:22:36,455] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:36,455] [INFO] Task started: Prodigal
[2024-01-25 20:22:36,456] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b834896-f5d0-467b-af1c-aca72c34e7aa/GCF_025149785.1_ASM2514978v1_genomic.fna.gz | prodigal -d GCF_025149785.1_ASM2514978v1_genomic.fna/cds.fna -a GCF_025149785.1_ASM2514978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:43,883] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:43,884] [INFO] Task started: HMMsearch
[2024-01-25 20:22:43,884] [INFO] Running command: hmmsearch --tblout GCF_025149785.1_ASM2514978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24971c5b-dc73-4d0b-8fd6-377558fe5dfe/dqc_reference/reference_markers.hmm GCF_025149785.1_ASM2514978v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:44,118] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:44,119] [INFO] Found 6/6 markers.
[2024-01-25 20:22:44,146] [INFO] Query marker FASTA was written to GCF_025149785.1_ASM2514978v1_genomic.fna/markers.fasta
[2024-01-25 20:22:44,146] [INFO] Task started: Blastn
[2024-01-25 20:22:44,146] [INFO] Running command: blastn -query GCF_025149785.1_ASM2514978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24971c5b-dc73-4d0b-8fd6-377558fe5dfe/dqc_reference/reference_markers.fasta -out GCF_025149785.1_ASM2514978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:44,758] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:44,773] [INFO] Selected 22 target genomes.
[2024-01-25 20:22:44,773] [INFO] Target genome list was writen to GCF_025149785.1_ASM2514978v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:44,794] [INFO] Task started: fastANI
[2024-01-25 20:22:44,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b834896-f5d0-467b-af1c-aca72c34e7aa/GCF_025149785.1_ASM2514978v1_genomic.fna.gz --refList GCF_025149785.1_ASM2514978v1_genomic.fna/target_genomes.txt --output GCF_025149785.1_ASM2514978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:56,826] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:56,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24971c5b-dc73-4d0b-8fd6-377558fe5dfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:56,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24971c5b-dc73-4d0b-8fd6-377558fe5dfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:56,839] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:22:56,839] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:22:56,839] [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
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	100.0	1124	1124	95	conclusive
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	85.0028	269	1124	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	83.1863	210	1124	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	81.7925	172	1124	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	80.9711	145	1124	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	80.5363	160	1124	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	80.4956	206	1124	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	80.3617	219	1124	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	80.3519	220	1124	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	80.2444	164	1124	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	80.1769	255	1124	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	80.1537	220	1124	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	80.1408	154	1124	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	80.0846	253	1124	95	below_threshold
Anaerostipes caccae	strain=DSM 14662	GCA_025146005.1	105841	105841	type	True	79.9324	55	1124	95	below_threshold
Anaerostipes caccae	strain=JCM 13470	GCA_014467075.1	105841	105841	type	True	79.7695	54	1124	95	below_threshold
Bariatricus massiliensis	strain=AT12	GCA_900086725.1	1745713	1745713	type	True	79.6749	168	1124	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	79.667	205	1124	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	79.389	100	1124	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	79.3387	121	1124	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	79.2969	149	1124	95	below_threshold
Sellimonas intestinalis	strain=BR72	GCA_001280875.1	1653434	1653434	type	True	77.6933	124	1124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:56,840] [INFO] DFAST Taxonomy check result was written to GCF_025149785.1_ASM2514978v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:56,841] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:56,841] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:56,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24971c5b-dc73-4d0b-8fd6-377558fe5dfe/dqc_reference/checkm_data
[2024-01-25 20:22:56,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:56,876] [INFO] Task started: CheckM
[2024-01-25 20:22:56,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025149785.1_ASM2514978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025149785.1_ASM2514978v1_genomic.fna/checkm_input GCF_025149785.1_ASM2514978v1_genomic.fna/checkm_result
[2024-01-25 20:23:23,532] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:23,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:23,551] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:23,552] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:23,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025149785.1_ASM2514978v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:23,552] [INFO] Task started: Blastn
[2024-01-25 20:23:23,552] [INFO] Running command: blastn -query GCF_025149785.1_ASM2514978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24971c5b-dc73-4d0b-8fd6-377558fe5dfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_025149785.1_ASM2514978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:24,652] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:24,654] [INFO] Selected 18 target genomes.
[2024-01-25 20:23:24,655] [INFO] Target genome list was writen to GCF_025149785.1_ASM2514978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:24,672] [INFO] Task started: fastANI
[2024-01-25 20:23:24,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b834896-f5d0-467b-af1c-aca72c34e7aa/GCF_025149785.1_ASM2514978v1_genomic.fna.gz --refList GCF_025149785.1_ASM2514978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025149785.1_ASM2514978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:23:34,700] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:34,710] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:23:34,711] [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
GCA_000155875.1	s__Bariatricus comes	99.9102	1071	1124	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	conclusive
GCF_013300725.1	s__Bariatricus comes_A	94.9733	808	1124	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_001312505.1	s__Mediterraneibacter faecis	83.3105	289	1124	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.72	95.03	0.76	0.67	61	-
GCF_001404875.1	s__Dorea_A longicatena_B	82.2365	279	1124	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	-
GCF_003435815.1	s__CAG-317 sp000433215	82.0992	272	1124	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_014287635.1	s__1XD42-69 sp014287635	80.8545	145	1124	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	98.20	98.20	0.93	0.93	2	-
GCA_003480425.1	s__Schaedlerella sp900066545	80.6662	208	1124	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.16	96.52	0.81	0.77	11	-
GCF_008121495.1	s__Ruminococcus_B gnavus	80.3297	223	1124	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	-
GCA_900554415.1	s__Bariatricus sp900554415	79.251	156	1124	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.94	99.94	0.94	0.94	2	-
GCA_004560705.1	s__Bariatricus sp004560705	78.8539	242	1124	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.19	99.19	0.81	0.81	2	-
GCA_900550865.1	s__Dorea_A sp900550865	78.309	211	1124	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	-
GCF_016900655.1	s__Sellimonas avistercoris	78.0699	154	1124	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sellimonas	95.0	98.38	98.11	0.87	0.78	13	-
GCA_905216215.1	s__Bariatricus sp905216215	78.0055	148	1124	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015560805.1	s__Schaedlerella glycyrrhizinilytica_A	77.967	145	1124	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.33	97.63	0.90	0.83	10	-
GCA_019116885.1	s__Mediterraneibacter pullistercoris	76.8739	79	1124	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.20	99.20	0.93	0.93	2	-
GCA_019119745.1	s__Mediterraneibacter gallistercoris	76.8508	81	1124	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_019119995.1	s__Mediterraneibacter faecavium	76.8113	91	1124	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.90	99.90	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:23:34,713] [INFO] GTDB search result was written to GCF_025149785.1_ASM2514978v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:34,714] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:34,720] [INFO] DFAST_QC result json was written to GCF_025149785.1_ASM2514978v1_genomic.fna/dqc_result.json
[2024-01-25 20:23:34,720] [INFO] DFAST_QC completed!
[2024-01-25 20:23:34,720] [INFO] Total running time: 0h0m59s