[2024-01-24 12:39:35,262] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,263] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,264] [INFO] DQC Reference Directory: /var/lib/cwl/stge2e808ff-e19a-46a0-aeb6-2efc2fb17975/dqc_reference
[2024-01-24 12:39:36,506] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,507] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,507] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4e6c333-1399-49f8-aef3-f666b94ee06c/GCF_001754075.1_ASM175407v1_genomic.fna.gz | prodigal -d GCF_001754075.1_ASM175407v1_genomic.fna/cds.fna -a GCF_001754075.1_ASM175407v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:44,632] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:44,633] [INFO] Task started: HMMsearch
[2024-01-24 12:39:44,633] [INFO] Running command: hmmsearch --tblout GCF_001754075.1_ASM175407v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2e808ff-e19a-46a0-aeb6-2efc2fb17975/dqc_reference/reference_markers.hmm GCF_001754075.1_ASM175407v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:44,907] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:44,910] [INFO] Found 6/6 markers.
[2024-01-24 12:39:44,941] [INFO] Query marker FASTA was written to GCF_001754075.1_ASM175407v1_genomic.fna/markers.fasta
[2024-01-24 12:39:44,942] [INFO] Task started: Blastn
[2024-01-24 12:39:44,942] [INFO] Running command: blastn -query GCF_001754075.1_ASM175407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2e808ff-e19a-46a0-aeb6-2efc2fb17975/dqc_reference/reference_markers.fasta -out GCF_001754075.1_ASM175407v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:45,587] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:45,591] [INFO] Selected 24 target genomes.
[2024-01-24 12:39:45,591] [INFO] Target genome list was writen to GCF_001754075.1_ASM175407v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:45,599] [INFO] Task started: fastANI
[2024-01-24 12:39:45,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4e6c333-1399-49f8-aef3-f666b94ee06c/GCF_001754075.1_ASM175407v1_genomic.fna.gz --refList GCF_001754075.1_ASM175407v1_genomic.fna/target_genomes.txt --output GCF_001754075.1_ASM175407v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:39:58,837] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:58,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2e808ff-e19a-46a0-aeb6-2efc2fb17975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:39:58,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2e808ff-e19a-46a0-aeb6-2efc2fb17975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:39:58,855] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:39:58,855] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:39:58,855] [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
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	100.0	1074	1075	95	conclusive
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	81.2189	281	1075	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	78.6101	92	1075	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	78.4387	225	1075	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	78.4237	224	1075	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_000425525.1	438033	438033	type	True	78.2757	62	1075	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	78.185	79	1075	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	77.8848	60	1075	95	below_threshold
Sellimonas caecigallum	strain=SW451	GCA_019754295.1	2592333	2592333	type	True	77.8836	122	1075	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	77.8466	167	1075	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	77.8168	173	1075	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	77.7991	178	1075	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.7661	79	1075	95	below_threshold
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	77.7234	197	1075	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.2156	142	1075	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.1689	141	1075	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.1074	139	1075	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	76.6991	53	1075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:39:58,857] [INFO] DFAST Taxonomy check result was written to GCF_001754075.1_ASM175407v1_genomic.fna/tc_result.tsv
[2024-01-24 12:39:58,858] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:39:58,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:39:58,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2e808ff-e19a-46a0-aeb6-2efc2fb17975/dqc_reference/checkm_data
[2024-01-24 12:39:58,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:39:58,897] [INFO] Task started: CheckM
[2024-01-24 12:39:58,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001754075.1_ASM175407v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001754075.1_ASM175407v1_genomic.fna/checkm_input GCF_001754075.1_ASM175407v1_genomic.fna/checkm_result
[2024-01-24 12:40:29,522] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:29,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:29,546] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:29,547] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:29,547] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001754075.1_ASM175407v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:29,548] [INFO] Task started: Blastn
[2024-01-24 12:40:29,548] [INFO] Running command: blastn -query GCF_001754075.1_ASM175407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2e808ff-e19a-46a0-aeb6-2efc2fb17975/dqc_reference/reference_markers_gtdb.fasta -out GCF_001754075.1_ASM175407v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:30,674] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:30,679] [INFO] Selected 18 target genomes.
[2024-01-24 12:40:30,679] [INFO] Target genome list was writen to GCF_001754075.1_ASM175407v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:30,689] [INFO] Task started: fastANI
[2024-01-24 12:40:30,689] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4e6c333-1399-49f8-aef3-f666b94ee06c/GCF_001754075.1_ASM175407v1_genomic.fna.gz --refList GCF_001754075.1_ASM175407v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001754075.1_ASM175407v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:41,733] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:41,752] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:41,752] [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_001754075.1	s__Merdimonas faecis	100.0	1074	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	98.52	97.96	0.90	0.84	10	conclusive
GCF_016902415.1	s__Merdimonas massiliensis	81.954	493	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	97.93	97.91	0.86	0.83	3	-
GCA_900553355.1	s__Merdimonas sp900553355	81.5936	530	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902406105.1	s__Massilistercora sp902406105	78.686	223	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Massilistercora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295125.1	s__Clostridium_AP scindens	78.4568	224	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP	95.0	99.44	99.12	0.90	0.78	13	-
GCF_003435815.1	s__CAG-317 sp000433215	78.2693	180	1075	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	-
GCA_910574885.1	s__Sporofaciens sp910574885	77.9535	190	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	99.41	98.81	0.91	0.83	5	-
GCA_910575835.1	s__Sporofaciens sp910575835	77.9315	216	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119995.1	s__Mediterraneibacter faecavium	77.8793	112	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.90	99.90	0.92	0.92	2	-
GCA_019114065.1	s__Massilistercora gallistercoris	77.845	189	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Massilistercora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154065.1	s__Dorea_A longicatena	77.8168	173	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	98.55	97.61	0.85	0.69	49	-
GCF_900240315.1	s__Dorea_B phocaeensis	77.7991	178	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_B	95.0	98.22	97.28	0.87	0.81	8	-
GCA_910575605.1	s__UBA7109 sp910575605	77.5418	150	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	99.27	99.27	0.93	0.93	2	-
GCA_004560705.1	s__Bariatricus sp004560705	77.4208	112	1075	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	77.3963	152	1075	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_910584615.1	s__MD308 sp910584615	77.1623	138	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589275.1	s__Lachnoclostridium_B sp910589275	77.1229	118	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575475.1	s__Schaedlerella sp910575475	77.119	156	1075	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.35	99.35	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:41,754] [INFO] GTDB search result was written to GCF_001754075.1_ASM175407v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:41,755] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:41,760] [INFO] DFAST_QC result json was written to GCF_001754075.1_ASM175407v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:41,760] [INFO] DFAST_QC completed!
[2024-01-24 12:40:41,760] [INFO] Total running time: 0h1m6s