[2023-06-29 19:25:15,503] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:25:15,506] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:25:15,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg14a6c3f2-2b49-4a16-ba74-94916b9c4283/dqc_reference
[2023-06-29 19:25:16,697] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:25:16,698] [INFO] Task started: Prodigal
[2023-06-29 19:25:16,699] [INFO] Running command: gunzip -c /var/lib/cwl/stg30b6b6ea-953c-4107-9b93-2bb4e03e1694/GCA_023417875.1_ASM2341787v1_genomic.fna.gz | prodigal -d GCA_023417875.1_ASM2341787v1_genomic.fna/cds.fna -a GCA_023417875.1_ASM2341787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:25:28,651] [INFO] Task succeeded: Prodigal
[2023-06-29 19:25:28,652] [INFO] Task started: HMMsearch
[2023-06-29 19:25:28,652] [INFO] Running command: hmmsearch --tblout GCA_023417875.1_ASM2341787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14a6c3f2-2b49-4a16-ba74-94916b9c4283/dqc_reference/reference_markers.hmm GCA_023417875.1_ASM2341787v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:25:28,961] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:25:28,962] [INFO] Found 6/6 markers.
[2023-06-29 19:25:29,007] [INFO] Query marker FASTA was written to GCA_023417875.1_ASM2341787v1_genomic.fna/markers.fasta
[2023-06-29 19:25:29,007] [INFO] Task started: Blastn
[2023-06-29 19:25:29,007] [INFO] Running command: blastn -query GCA_023417875.1_ASM2341787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14a6c3f2-2b49-4a16-ba74-94916b9c4283/dqc_reference/reference_markers.fasta -out GCA_023417875.1_ASM2341787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:25:29,587] [INFO] Task succeeded: Blastn
[2023-06-29 19:25:29,592] [INFO] Selected 21 target genomes.
[2023-06-29 19:25:29,592] [INFO] Target genome list was writen to GCA_023417875.1_ASM2341787v1_genomic.fna/target_genomes.txt
[2023-06-29 19:25:29,594] [INFO] Task started: fastANI
[2023-06-29 19:25:29,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg30b6b6ea-953c-4107-9b93-2bb4e03e1694/GCA_023417875.1_ASM2341787v1_genomic.fna.gz --refList GCA_023417875.1_ASM2341787v1_genomic.fna/target_genomes.txt --output GCA_023417875.1_ASM2341787v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:25:43,282] [INFO] Task succeeded: fastANI
[2023-06-29 19:25:43,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14a6c3f2-2b49-4a16-ba74-94916b9c4283/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:25:43,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14a6c3f2-2b49-4a16-ba74-94916b9c4283/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:25:43,296] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:25:43,296] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:25:43,297] [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
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	79.3641	577	1803	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	79.1631	533	1803	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	79.0626	540	1803	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	79.014	543	1803	95	below_threshold
Lacrimispora algidixylanolytica	strain=SPL73	GCA_003609635.1	94868	94868	type	True	78.6013	527	1803	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	78.1684	234	1803	95	below_threshold
Anaerocolumna jejuensis	strain=DSM 15929	GCA_900142215.1	259063	259063	type	True	76.4271	87	1803	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	76.3877	105	1803	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	76.387	103	1803	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	76.3381	105	1803	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	76.1075	68	1803	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	75.9988	56	1803	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	75.9343	57	1803	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:25:43,299] [INFO] DFAST Taxonomy check result was written to GCA_023417875.1_ASM2341787v1_genomic.fna/tc_result.tsv
[2023-06-29 19:25:43,299] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:25:43,299] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:25:43,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14a6c3f2-2b49-4a16-ba74-94916b9c4283/dqc_reference/checkm_data
[2023-06-29 19:25:43,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:25:43,355] [INFO] Task started: CheckM
[2023-06-29 19:25:43,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023417875.1_ASM2341787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023417875.1_ASM2341787v1_genomic.fna/checkm_input GCA_023417875.1_ASM2341787v1_genomic.fna/checkm_result
[2023-06-29 19:26:23,132] [INFO] Task succeeded: CheckM
[2023-06-29 19:26:23,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 19:26:23,161] [INFO] ===== Completeness check finished =====
[2023-06-29 19:26:23,162] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:26:23,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023417875.1_ASM2341787v1_genomic.fna/markers.fasta)
[2023-06-29 19:26:23,162] [INFO] Task started: Blastn
[2023-06-29 19:26:23,162] [INFO] Running command: blastn -query GCA_023417875.1_ASM2341787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14a6c3f2-2b49-4a16-ba74-94916b9c4283/dqc_reference/reference_markers_gtdb.fasta -out GCA_023417875.1_ASM2341787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:26:23,940] [INFO] Task succeeded: Blastn
[2023-06-29 19:26:23,946] [INFO] Selected 8 target genomes.
[2023-06-29 19:26:23,946] [INFO] Target genome list was writen to GCA_023417875.1_ASM2341787v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:26:23,949] [INFO] Task started: fastANI
[2023-06-29 19:26:23,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg30b6b6ea-953c-4107-9b93-2bb4e03e1694/GCA_023417875.1_ASM2341787v1_genomic.fna.gz --refList GCA_023417875.1_ASM2341787v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023417875.1_ASM2341787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:26:34,172] [INFO] Task succeeded: fastANI
[2023-06-29 19:26:34,183] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:26:34,183] [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_002934545.1	s__Lacrimispora xylanolytica	98.6929	1646	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	98.92	98.92	0.97	0.97	2	conclusive
GCA_009712635.1	s__Lacrimispora sp009712635	94.7113	1544	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017084465.1	s__Lacrimispora xylanolytica_B	94.2857	1492	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.07	99.07	0.96	0.96	2	-
GCA_015057705.1	s__Lacrimispora sp015057705	94.1644	1259	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057775.1	s__Lacrimispora sp015057775	94.1635	1111	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013036995.1	s__Lacrimispora xylanolytica_A	93.986	1355	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057715.1	s__Lacrimispora sp015057715	93.7942	1311	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432035.1	s__Lacrimispora indica	87.0544	1254	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:26:34,185] [INFO] GTDB search result was written to GCA_023417875.1_ASM2341787v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:26:34,185] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:26:34,189] [INFO] DFAST_QC result json was written to GCA_023417875.1_ASM2341787v1_genomic.fna/dqc_result.json
[2023-06-29 19:26:34,189] [INFO] DFAST_QC completed!
[2023-06-29 19:26:34,189] [INFO] Total running time: 0h1m19s