[2023-06-30 03:32:46,443] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:32:46,445] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:32:46,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bb64bdc-e7f0-43d0-8846-30f6a7366567/dqc_reference
[2023-06-30 03:32:47,659] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:32:47,660] [INFO] Task started: Prodigal
[2023-06-30 03:32:47,660] [INFO] Running command: gunzip -c /var/lib/cwl/stg99835e3c-bbbb-40e3-bb85-83fb177ffe7d/GCA_008669205.1_ASM866920v1_genomic.fna.gz | prodigal -d GCA_008669205.1_ASM866920v1_genomic.fna/cds.fna -a GCA_008669205.1_ASM866920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:32:54,617] [INFO] Task succeeded: Prodigal
[2023-06-30 03:32:54,618] [INFO] Task started: HMMsearch
[2023-06-30 03:32:54,618] [INFO] Running command: hmmsearch --tblout GCA_008669205.1_ASM866920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bb64bdc-e7f0-43d0-8846-30f6a7366567/dqc_reference/reference_markers.hmm GCA_008669205.1_ASM866920v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:32:54,911] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:32:54,913] [INFO] Found 6/6 markers.
[2023-06-30 03:32:54,944] [INFO] Query marker FASTA was written to GCA_008669205.1_ASM866920v1_genomic.fna/markers.fasta
[2023-06-30 03:32:54,945] [INFO] Task started: Blastn
[2023-06-30 03:32:54,945] [INFO] Running command: blastn -query GCA_008669205.1_ASM866920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bb64bdc-e7f0-43d0-8846-30f6a7366567/dqc_reference/reference_markers.fasta -out GCA_008669205.1_ASM866920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:32:55,589] [INFO] Task succeeded: Blastn
[2023-06-30 03:32:55,594] [INFO] Selected 19 target genomes.
[2023-06-30 03:32:55,595] [INFO] Target genome list was writen to GCA_008669205.1_ASM866920v1_genomic.fna/target_genomes.txt
[2023-06-30 03:32:55,596] [INFO] Task started: fastANI
[2023-06-30 03:32:55,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg99835e3c-bbbb-40e3-bb85-83fb177ffe7d/GCA_008669205.1_ASM866920v1_genomic.fna.gz --refList GCA_008669205.1_ASM866920v1_genomic.fna/target_genomes.txt --output GCA_008669205.1_ASM866920v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:33:05,255] [INFO] Task succeeded: fastANI
[2023-06-30 03:33:05,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bb64bdc-e7f0-43d0-8846-30f6a7366567/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:33:05,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bb64bdc-e7f0-43d0-8846-30f6a7366567/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:33:05,277] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:33:05,277] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:33:05,277] [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
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	81.7005	135	986	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	81.0332	172	986	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	80.9549	126	986	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	80.4302	342	986	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	80.4027	340	986	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	80.2866	226	986	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	80.1795	220	986	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	80.1738	190	986	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	80.1375	227	986	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	80.1146	233	986	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	80.087	217	986	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	79.9587	215	986	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.5243	165	986	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	79.4599	225	986	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	78.6314	172	986	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.3009	90	986	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	78.2115	185	986	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.6123	112	986	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:33:05,279] [INFO] DFAST Taxonomy check result was written to GCA_008669205.1_ASM866920v1_genomic.fna/tc_result.tsv
[2023-06-30 03:33:05,280] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:33:05,280] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:33:05,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bb64bdc-e7f0-43d0-8846-30f6a7366567/dqc_reference/checkm_data
[2023-06-30 03:33:05,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:33:05,317] [INFO] Task started: CheckM
[2023-06-30 03:33:05,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_008669205.1_ASM866920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_008669205.1_ASM866920v1_genomic.fna/checkm_input GCA_008669205.1_ASM866920v1_genomic.fna/checkm_result
[2023-06-30 03:33:32,709] [INFO] Task succeeded: CheckM
[2023-06-30 03:33:32,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:33:32,732] [INFO] ===== Completeness check finished =====
[2023-06-30 03:33:32,732] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:33:32,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_008669205.1_ASM866920v1_genomic.fna/markers.fasta)
[2023-06-30 03:33:32,733] [INFO] Task started: Blastn
[2023-06-30 03:33:32,733] [INFO] Running command: blastn -query GCA_008669205.1_ASM866920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bb64bdc-e7f0-43d0-8846-30f6a7366567/dqc_reference/reference_markers_gtdb.fasta -out GCA_008669205.1_ASM866920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:33:33,794] [INFO] Task succeeded: Blastn
[2023-06-30 03:33:33,799] [INFO] Selected 21 target genomes.
[2023-06-30 03:33:33,799] [INFO] Target genome list was writen to GCA_008669205.1_ASM866920v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:33:33,801] [INFO] Task started: fastANI
[2023-06-30 03:33:33,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg99835e3c-bbbb-40e3-bb85-83fb177ffe7d/GCA_008669205.1_ASM866920v1_genomic.fna.gz --refList GCA_008669205.1_ASM866920v1_genomic.fna/target_genomes_gtdb.txt --output GCA_008669205.1_ASM866920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:33:43,758] [INFO] Task succeeded: fastANI
[2023-06-30 03:33:43,779] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:33:43,779] [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_001312505.1	s__Mediterraneibacter faecis	96.4146	739	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.72	95.03	0.76	0.67	61	conclusive
GCA_003480425.1	s__Schaedlerella sp900066545	82.6329	301	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.16	96.52	0.81	0.77	11	-
GCA_900554415.1	s__Bariatricus sp900554415	80.5291	82	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.94	99.94	0.94	0.94	2	-
GCF_000155205.1	s__Mediterraneibacter lactaris	80.4243	338	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCF_008121495.1	s__Ruminococcus_B gnavus	80.0902	234	986	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	79.9252	240	986	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_000155875.1	s__Bariatricus comes	79.3593	221	986	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_900544395.1	s__Ruminococcus_B sp900544395	78.6782	177	986	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_002159505.1	s__Mediterraneibacter ornithocaccae	78.6252	184	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.93	97.52	0.83	0.82	3	-
GCF_018228665.1	s__UBA9414 sp003458885	78.2898	121	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	97.84	97.84	0.85	0.85	3	-
GCA_905203555.1	s__Schaedlerella sp905203555	78.254	161	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904419285.1	s__Mediterraneibacter caccogallinarum	78.0484	158	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.44	97.89	0.90	0.83	10	-
GCA_900751785.1	s__Mediterraneibacter faecigallinarum	77.9799	142	986	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_019113645.1	s__Mediterraneibacter vanvlietii	77.8657	186	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.04	97.81	0.84	0.83	3	-
GCA_019118885.1	s__Mediterraneibacter surreyensis	77.7282	142	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.86	98.12	0.80	0.76	3	-
GCA_019119675.1	s__Mediterraneibacter faecipullorum	77.5286	162	986	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_019119745.1	s__Mediterraneibacter gallistercoris	77.4792	133	986	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	77.3541	144	986	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_018365895.1	s__UBA9414 sp018365895	77.0443	106	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116845.1	s__Mediterraneibacter stercoravium	76.9622	117	986	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.54	97.95	0.86	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-30 03:33:43,781] [INFO] GTDB search result was written to GCA_008669205.1_ASM866920v1_genomic.fna/result_gtdb.tsv
[2023-06-30 03:33:43,782] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:33:43,786] [INFO] DFAST_QC result json was written to GCA_008669205.1_ASM866920v1_genomic.fna/dqc_result.json
[2023-06-30 03:33:43,787] [INFO] DFAST_QC completed!
[2023-06-30 03:33:43,787] [INFO] Total running time: 0h0m57s