[2024-01-24 11:05:27,714] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:27,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:27,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg414d01dc-17d0-4b0b-add4-0040702710b1/dqc_reference
[2024-01-24 11:05:29,133] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,134] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,134] [INFO] Running command: gunzip -c /var/lib/cwl/stga83e5d2a-d740-41b0-b738-93fe2dec403a/GCF_014385005.1_ASM1438500v1_genomic.fna.gz | prodigal -d GCF_014385005.1_ASM1438500v1_genomic.fna/cds.fna -a GCF_014385005.1_ASM1438500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:38,508] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:38,509] [INFO] Task started: HMMsearch
[2024-01-24 11:05:38,509] [INFO] Running command: hmmsearch --tblout GCF_014385005.1_ASM1438500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg414d01dc-17d0-4b0b-add4-0040702710b1/dqc_reference/reference_markers.hmm GCF_014385005.1_ASM1438500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:38,889] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:38,890] [INFO] Found 6/6 markers.
[2024-01-24 11:05:38,935] [INFO] Query marker FASTA was written to GCF_014385005.1_ASM1438500v1_genomic.fna/markers.fasta
[2024-01-24 11:05:38,936] [INFO] Task started: Blastn
[2024-01-24 11:05:38,936] [INFO] Running command: blastn -query GCF_014385005.1_ASM1438500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg414d01dc-17d0-4b0b-add4-0040702710b1/dqc_reference/reference_markers.fasta -out GCF_014385005.1_ASM1438500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:39,663] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:39,666] [INFO] Selected 23 target genomes.
[2024-01-24 11:05:39,666] [INFO] Target genome list was writen to GCF_014385005.1_ASM1438500v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:39,673] [INFO] Task started: fastANI
[2024-01-24 11:05:39,674] [INFO] Running command: fastANI --query /var/lib/cwl/stga83e5d2a-d740-41b0-b738-93fe2dec403a/GCF_014385005.1_ASM1438500v1_genomic.fna.gz --refList GCF_014385005.1_ASM1438500v1_genomic.fna/target_genomes.txt --output GCF_014385005.1_ASM1438500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:53,883] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:53,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg414d01dc-17d0-4b0b-add4-0040702710b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:53,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg414d01dc-17d0-4b0b-add4-0040702710b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:53,900] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:53,900] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:53,900] [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
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	100.0	1177	1181	95	conclusive
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	81.4494	185	1181	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	81.0875	198	1181	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	80.9446	189	1181	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	80.5268	154	1181	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	80.3767	195	1181	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	79.4808	115	1181	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	79.2235	111	1181	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	79.1862	104	1181	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	79.0932	108	1181	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	79.0231	107	1181	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	79.0227	105	1181	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	78.8775	122	1181	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	78.8129	91	1181	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	78.4078	64	1181	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	78.4025	79	1181	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.8416	92	1181	95	below_threshold
Bariatricus massiliensis	strain=AT12	GCA_900086725.1	1745713	1745713	type	True	77.6089	62	1181	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.4082	76	1181	95	below_threshold
Konateibacter massiliensis	strain=Marseille-P3773	GCA_900184995.1	2002841	2002841	type	True	76.7972	52	1181	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:53,902] [INFO] DFAST Taxonomy check result was written to GCF_014385005.1_ASM1438500v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:53,902] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:53,903] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:53,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg414d01dc-17d0-4b0b-add4-0040702710b1/dqc_reference/checkm_data
[2024-01-24 11:05:53,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:53,945] [INFO] Task started: CheckM
[2024-01-24 11:05:53,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014385005.1_ASM1438500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014385005.1_ASM1438500v1_genomic.fna/checkm_input GCF_014385005.1_ASM1438500v1_genomic.fna/checkm_result
[2024-01-24 11:06:27,135] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:27,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:27,158] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:27,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:27,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014385005.1_ASM1438500v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:27,159] [INFO] Task started: Blastn
[2024-01-24 11:06:27,160] [INFO] Running command: blastn -query GCF_014385005.1_ASM1438500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg414d01dc-17d0-4b0b-add4-0040702710b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014385005.1_ASM1438500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:28,287] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:28,291] [INFO] Selected 18 target genomes.
[2024-01-24 11:06:28,291] [INFO] Target genome list was writen to GCF_014385005.1_ASM1438500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:28,304] [INFO] Task started: fastANI
[2024-01-24 11:06:28,304] [INFO] Running command: fastANI --query /var/lib/cwl/stga83e5d2a-d740-41b0-b738-93fe2dec403a/GCF_014385005.1_ASM1438500v1_genomic.fna.gz --refList GCF_014385005.1_ASM1438500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014385005.1_ASM1438500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:40,278] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:40,297] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:40,297] [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_014385005.1	s__Marvinbryantia sp014385005	100.0	1177	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	98.94	98.94	0.98	0.98	2	conclusive
GCA_900544685.1	s__Marvinbryantia sp900544685	93.5343	776	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003435055.1	s__Marvinbryantia sp900066075	85.4115	722	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	98.92	97.84	0.90	0.80	3	-
GCA_902363685.1	s__UMGS1375 sp900066615	80.6364	201	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375	95.0	98.15	97.87	0.85	0.79	16	-
GCF_013304385.1	s__Blautia_A sp900066505	80.1724	160	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.06	97.97	0.82	0.78	4	-
GCF_003479605.1	s__RUG115 sp900066395	80.1143	108	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	98.27	97.78	0.88	0.83	29	-
GCA_900765975.1	s__Schaedlerella sp900765975	77.9973	61	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.94	99.94	0.80	0.80	2	-
GCA_002361775.1	s__Oliverpabstia sp002361775	77.9446	92	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	99.87	99.86	0.91	0.89	3	-
GCA_016297895.1	s__Marvinbryantia sp016297895	77.7555	165	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004560705.1	s__Bariatricus sp004560705	77.7215	76	1181	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_900539525.1	s__CAG-56 sp900539525	77.4784	107	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.91	99.91	0.93	0.93	2	-
GCA_018365455.1	s__Robinsoniella sp900555455	77.2955	119	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Robinsoniella	95.0	99.95	99.95	0.97	0.97	2	-
GCF_000797495.1	s__Robinsoniella peoriensis	77.2313	109	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Robinsoniella	95.0	98.88	98.73	0.91	0.88	7	-
GCA_900752065.1	s__CAG-56 sp900752065	77.1709	79	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.98	99.98	0.94	0.94	2	-
GCA_900316115.1	s__Blautia_A sp900316115	77.0865	94	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.53	99.48	0.92	0.90	3	-
GCA_002473385.1	s__Marvinbryantia sp002473385	76.7242	99	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713105.1	s__Limivivens merdigallinarum	76.6443	66	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.32	98.32	0.87	0.87	2	-
GCA_905207905.1	s__Merdiplasma sp905207905	76.3468	57	1181	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:40,299] [INFO] GTDB search result was written to GCF_014385005.1_ASM1438500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:40,300] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:40,304] [INFO] DFAST_QC result json was written to GCF_014385005.1_ASM1438500v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:40,304] [INFO] DFAST_QC completed!
[2024-01-24 11:06:40,304] [INFO] Total running time: 0h1m13s