[2023-06-13 10:22:21,920] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:22:21,922] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:22:21,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg40b34b10-f763-4cd4-975d-a7d721853036/dqc_reference
[2023-06-13 10:22:24,283] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:22:24,284] [INFO] Task started: Prodigal
[2023-06-13 10:22:24,284] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a9a1064-c45a-4672-b560-bff059ae45e7/GCA_022764425.1_ASM2276442v1_genomic.fna.gz | prodigal -d GCA_022764425.1_ASM2276442v1_genomic.fna/cds.fna -a GCA_022764425.1_ASM2276442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:22:30,361] [INFO] Task succeeded: Prodigal
[2023-06-13 10:22:30,361] [INFO] Task started: HMMsearch
[2023-06-13 10:22:30,361] [INFO] Running command: hmmsearch --tblout GCA_022764425.1_ASM2276442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40b34b10-f763-4cd4-975d-a7d721853036/dqc_reference/reference_markers.hmm GCA_022764425.1_ASM2276442v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:22:30,647] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:22:30,648] [INFO] Found 6/6 markers.
[2023-06-13 10:22:30,680] [INFO] Query marker FASTA was written to GCA_022764425.1_ASM2276442v1_genomic.fna/markers.fasta
[2023-06-13 10:22:30,681] [INFO] Task started: Blastn
[2023-06-13 10:22:30,681] [INFO] Running command: blastn -query GCA_022764425.1_ASM2276442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40b34b10-f763-4cd4-975d-a7d721853036/dqc_reference/reference_markers.fasta -out GCA_022764425.1_ASM2276442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:22:31,418] [INFO] Task succeeded: Blastn
[2023-06-13 10:22:31,423] [INFO] Selected 19 target genomes.
[2023-06-13 10:22:31,424] [INFO] Target genome list was writen to GCA_022764425.1_ASM2276442v1_genomic.fna/target_genomes.txt
[2023-06-13 10:22:31,425] [INFO] Task started: fastANI
[2023-06-13 10:22:31,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a9a1064-c45a-4672-b560-bff059ae45e7/GCA_022764425.1_ASM2276442v1_genomic.fna.gz --refList GCA_022764425.1_ASM2276442v1_genomic.fna/target_genomes.txt --output GCA_022764425.1_ASM2276442v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:22:40,848] [INFO] Task succeeded: fastANI
[2023-06-13 10:22:40,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40b34b10-f763-4cd4-975d-a7d721853036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:22:40,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40b34b10-f763-4cd4-975d-a7d721853036/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:22:40,863] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 10:22:40,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 10:22:40,863] [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
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	99.4672	704	761	95	conclusive
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.9277	169	761	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.7119	157	761	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.6235	162	761	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	77.6182	188	761	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.6132	163	761	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	76.92	86	761	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	76.7596	64	761	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	76.524	91	761	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	76.499	56	761	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	76.4775	52	761	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	76.3876	63	761	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	76.3829	63	761	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	76.3792	62	761	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	76.3792	62	761	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:22:40,866] [INFO] DFAST Taxonomy check result was written to GCA_022764425.1_ASM2276442v1_genomic.fna/tc_result.tsv
[2023-06-13 10:22:40,867] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:22:40,867] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:22:40,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40b34b10-f763-4cd4-975d-a7d721853036/dqc_reference/checkm_data
[2023-06-13 10:22:40,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:22:40,902] [INFO] Task started: CheckM
[2023-06-13 10:22:40,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022764425.1_ASM2276442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022764425.1_ASM2276442v1_genomic.fna/checkm_input GCA_022764425.1_ASM2276442v1_genomic.fna/checkm_result
[2023-06-13 10:23:08,232] [INFO] Task succeeded: CheckM
[2023-06-13 10:23:08,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:23:08,259] [INFO] ===== Completeness check finished =====
[2023-06-13 10:23:08,260] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:23:08,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022764425.1_ASM2276442v1_genomic.fna/markers.fasta)
[2023-06-13 10:23:08,261] [INFO] Task started: Blastn
[2023-06-13 10:23:08,261] [INFO] Running command: blastn -query GCA_022764425.1_ASM2276442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40b34b10-f763-4cd4-975d-a7d721853036/dqc_reference/reference_markers_gtdb.fasta -out GCA_022764425.1_ASM2276442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:23:09,313] [INFO] Task succeeded: Blastn
[2023-06-13 10:23:09,325] [INFO] Selected 18 target genomes.
[2023-06-13 10:23:09,326] [INFO] Target genome list was writen to GCA_022764425.1_ASM2276442v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:23:09,336] [INFO] Task started: fastANI
[2023-06-13 10:23:09,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a9a1064-c45a-4672-b560-bff059ae45e7/GCA_022764425.1_ASM2276442v1_genomic.fna.gz --refList GCA_022764425.1_ASM2276442v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022764425.1_ASM2276442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:23:18,710] [INFO] Task succeeded: fastANI
[2023-06-13 10:23:18,736] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:23:18,736] [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_009695765.1	s__VUNI01 sp009695765	99.4672	704	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VUNI01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900552085.1	s__Agathobacter sp900552085	78.1527	147	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCF_001940165.1	s__Roseburia sp001940165	78.0894	149	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363675.1	s__Agathobacter sp000434275	77.9705	199	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.18	99.14	0.93	0.89	5	-
GCF_000174195.1	s__Roseburia inulinivorans	77.9486	168	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	-
GCA_017623935.1	s__Agathobacter sp017623935	77.7862	133	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.03	99.03	0.82	0.82	2	-
GCA_003483745.1	s__Roseburia sp003483745	77.734	152	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCA_900550545.1	s__Agathobacter sp900550545	77.7082	179	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001406815.1	s__Agathobacter faecis	77.6217	189	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.10	97.07	0.85	0.62	43	-
GCF_900537995.1	s__Roseburia intestinalis	77.6166	162	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	-
GCA_002474415.1	s__Agathobacter sp002474415	77.4979	130	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543445.1	s__Agathobacter sp900543445	77.4468	150	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.64	98.60	0.88	0.84	3	-
GCF_003470905.1	s__Roseburia sp003470905	77.4244	171	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCA_900550935.1	s__Roseburia sp900550935	77.2671	131	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.33	98.19	0.83	0.82	3	-
GCA_003507655.1	s__UBA11774 sp003507655	77.2594	99	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA11774	95.0	98.49	98.09	0.91	0.83	6	-
GCF_003122485.1	s__Eubacterium_I ramulus_A	76.9693	111	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	98.76	98.61	0.82	0.80	7	-
GCA_900316805.1	s__Agathobacter sp900316805	76.8607	97	761	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.85	99.74	0.94	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-13 10:23:18,740] [INFO] GTDB search result was written to GCA_022764425.1_ASM2276442v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:23:18,741] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:23:18,745] [INFO] DFAST_QC result json was written to GCA_022764425.1_ASM2276442v1_genomic.fna/dqc_result.json
[2023-06-13 10:23:18,745] [INFO] DFAST_QC completed!
[2023-06-13 10:23:18,745] [INFO] Total running time: 0h0m57s