[2023-06-16 19:07:28,802] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:07:28,804] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:07:28,804] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5373943-8a34-4ed9-9d2f-3d2935d6bf2e/dqc_reference
[2023-06-16 19:07:29,987] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:07:29,988] [INFO] Task started: Prodigal
[2023-06-16 19:07:29,988] [INFO] Running command: gunzip -c /var/lib/cwl/stgaea27cfe-08c3-4950-8818-0f341e1bfddc/GCA_028693705.1_ASM2869370v1_genomic.fna.gz | prodigal -d GCA_028693705.1_ASM2869370v1_genomic.fna/cds.fna -a GCA_028693705.1_ASM2869370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:07:35,864] [INFO] Task succeeded: Prodigal
[2023-06-16 19:07:35,865] [INFO] Task started: HMMsearch
[2023-06-16 19:07:35,865] [INFO] Running command: hmmsearch --tblout GCA_028693705.1_ASM2869370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5373943-8a34-4ed9-9d2f-3d2935d6bf2e/dqc_reference/reference_markers.hmm GCA_028693705.1_ASM2869370v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:07:36,098] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:07:36,099] [INFO] Found 6/6 markers.
[2023-06-16 19:07:36,129] [INFO] Query marker FASTA was written to GCA_028693705.1_ASM2869370v1_genomic.fna/markers.fasta
[2023-06-16 19:07:36,129] [INFO] Task started: Blastn
[2023-06-16 19:07:36,129] [INFO] Running command: blastn -query GCA_028693705.1_ASM2869370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5373943-8a34-4ed9-9d2f-3d2935d6bf2e/dqc_reference/reference_markers.fasta -out GCA_028693705.1_ASM2869370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:07:36,744] [INFO] Task succeeded: Blastn
[2023-06-16 19:07:36,747] [INFO] Selected 30 target genomes.
[2023-06-16 19:07:36,748] [INFO] Target genome list was writen to GCA_028693705.1_ASM2869370v1_genomic.fna/target_genomes.txt
[2023-06-16 19:07:36,783] [INFO] Task started: fastANI
[2023-06-16 19:07:36,783] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea27cfe-08c3-4950-8818-0f341e1bfddc/GCA_028693705.1_ASM2869370v1_genomic.fna.gz --refList GCA_028693705.1_ASM2869370v1_genomic.fna/target_genomes.txt --output GCA_028693705.1_ASM2869370v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:07:52,232] [INFO] Task succeeded: fastANI
[2023-06-16 19:07:52,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5373943-8a34-4ed9-9d2f-3d2935d6bf2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:07:52,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5373943-8a34-4ed9-9d2f-3d2935d6bf2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:07:52,240] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:07:52,240] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:07:52,241] [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	77.4142	52	956	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.2882	68	956	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	77.1071	56	956	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	77.0614	56	956	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	76.9681	50	956	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	76.8133	56	956	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	76.7433	59	956	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	76.7366	57	956	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	76.5664	52	956	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:07:52,242] [INFO] DFAST Taxonomy check result was written to GCA_028693705.1_ASM2869370v1_genomic.fna/tc_result.tsv
[2023-06-16 19:07:52,243] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:07:52,243] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:07:52,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5373943-8a34-4ed9-9d2f-3d2935d6bf2e/dqc_reference/checkm_data
[2023-06-16 19:07:52,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:07:52,280] [INFO] Task started: CheckM
[2023-06-16 19:07:52,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028693705.1_ASM2869370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028693705.1_ASM2869370v1_genomic.fna/checkm_input GCA_028693705.1_ASM2869370v1_genomic.fna/checkm_result
[2023-06-16 19:08:14,663] [INFO] Task succeeded: CheckM
[2023-06-16 19:08:14,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:08:14,681] [INFO] ===== Completeness check finished =====
[2023-06-16 19:08:14,681] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:08:14,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028693705.1_ASM2869370v1_genomic.fna/markers.fasta)
[2023-06-16 19:08:14,682] [INFO] Task started: Blastn
[2023-06-16 19:08:14,683] [INFO] Running command: blastn -query GCA_028693705.1_ASM2869370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5373943-8a34-4ed9-9d2f-3d2935d6bf2e/dqc_reference/reference_markers_gtdb.fasta -out GCA_028693705.1_ASM2869370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:08:15,678] [INFO] Task succeeded: Blastn
[2023-06-16 19:08:15,682] [INFO] Selected 31 target genomes.
[2023-06-16 19:08:15,683] [INFO] Target genome list was writen to GCA_028693705.1_ASM2869370v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:08:15,694] [INFO] Task started: fastANI
[2023-06-16 19:08:15,695] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea27cfe-08c3-4950-8818-0f341e1bfddc/GCA_028693705.1_ASM2869370v1_genomic.fna.gz --refList GCA_028693705.1_ASM2869370v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028693705.1_ASM2869370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:08:31,135] [INFO] Task succeeded: fastANI
[2023-06-16 19:08:31,148] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 19:08:31,149] [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_017623295.1	s__UBA3282 sp017623295	77.5085	116	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465845.1	s__Acetatifactor sp017465845	77.4494	61	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803415.1	s__CAG-95 sp014803415	77.4489	82	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	97.80	97.80	0.82	0.82	2	-
GCA_017463255.1	s__RGIG4034 sp017463255	77.1787	74	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG4034	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056915.1	s__Acetatifactor sp015056915	77.1259	62	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017434885.1	s__CAG-95 sp017434885	77.1228	85	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936885.1	s__UBA3282 sp017936885	77.0569	87	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804355.1	s__UBA3282 sp014804355	77.0395	50	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900753305.1	s__COE1 sp900753305	77.0064	95	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.96	99.96	0.93	0.93	2	-
GCA_017436865.1	s__COE1 sp017436865	76.975	81	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.13	98.13	0.76	0.76	2	-
GCA_002441865.1	s__CAG-194 sp002441865	76.8592	70	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-194	95.0	99.31	99.31	0.87	0.87	2	-
GCA_910585715.1	s__RGIG3040 sp910585715	76.7734	68	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3040	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017500935.1	s__Eisenbergiella sp017500935	76.7317	67	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612405.1	s__UBA3282 sp003612405	76.6438	68	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.19	99.19	0.85	0.85	2	-
GCA_017624235.1	s__JAAYNV01 sp017624235	76.6282	62	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAAYNV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017482205.1	s__CAG-510 sp017482205	76.5894	64	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	98.99	98.99	0.84	0.84	2	-
GCF_013300825.1	s__Blautia_A wexlerae_B	76.554	55	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCA_017555455.1	s__SFDP01 sp017555455	76.5277	74	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SFDP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017558145.1	s__SFDP01 sp017558145	76.4173	64	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SFDP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399445.1	s__RUG11237 sp017399445	76.3492	59	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11237	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017468395.1	s__SIG332 sp017468395	76.3183	58	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG332	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002492525.1	s__UBA3282 sp002492525	75.862	55	956	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.83	99.82	0.86	0.82	3	-
--------------------------------------------------------------------------------
[2023-06-16 19:08:31,152] [INFO] GTDB search result was written to GCA_028693705.1_ASM2869370v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:08:31,152] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:08:31,155] [INFO] DFAST_QC result json was written to GCA_028693705.1_ASM2869370v1_genomic.fna/dqc_result.json
[2023-06-16 19:08:31,156] [INFO] DFAST_QC completed!
[2023-06-16 19:08:31,156] [INFO] Total running time: 0h1m2s