[2023-06-30 22:23:00,664] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:23:00,666] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:23:00,666] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd4e5ebf-e4ea-4309-b7a5-280d10798f36/dqc_reference
[2023-06-30 22:23:03,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:23:03,759] [INFO] Task started: Prodigal
[2023-06-30 22:23:03,760] [INFO] Running command: gunzip -c /var/lib/cwl/stgeab5e83d-86da-476a-a196-bfb7815f9c13/GCA_019115265.1_ASM1911526v1_genomic.fna.gz | prodigal -d GCA_019115265.1_ASM1911526v1_genomic.fna/cds.fna -a GCA_019115265.1_ASM1911526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:23:10,841] [INFO] Task succeeded: Prodigal
[2023-06-30 22:23:10,841] [INFO] Task started: HMMsearch
[2023-06-30 22:23:10,841] [INFO] Running command: hmmsearch --tblout GCA_019115265.1_ASM1911526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd4e5ebf-e4ea-4309-b7a5-280d10798f36/dqc_reference/reference_markers.hmm GCA_019115265.1_ASM1911526v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:23:11,081] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:23:11,083] [INFO] Found 6/6 markers.
[2023-06-30 22:23:11,113] [INFO] Query marker FASTA was written to GCA_019115265.1_ASM1911526v1_genomic.fna/markers.fasta
[2023-06-30 22:23:11,114] [INFO] Task started: Blastn
[2023-06-30 22:23:11,114] [INFO] Running command: blastn -query GCA_019115265.1_ASM1911526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd4e5ebf-e4ea-4309-b7a5-280d10798f36/dqc_reference/reference_markers.fasta -out GCA_019115265.1_ASM1911526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:23:11,704] [INFO] Task succeeded: Blastn
[2023-06-30 22:23:11,709] [INFO] Selected 9 target genomes.
[2023-06-30 22:23:11,709] [INFO] Target genome list was writen to GCA_019115265.1_ASM1911526v1_genomic.fna/target_genomes.txt
[2023-06-30 22:23:11,711] [INFO] Task started: fastANI
[2023-06-30 22:23:11,711] [INFO] Running command: fastANI --query /var/lib/cwl/stgeab5e83d-86da-476a-a196-bfb7815f9c13/GCA_019115265.1_ASM1911526v1_genomic.fna.gz --refList GCA_019115265.1_ASM1911526v1_genomic.fna/target_genomes.txt --output GCA_019115265.1_ASM1911526v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:23:16,667] [INFO] Task succeeded: fastANI
[2023-06-30 22:23:16,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd4e5ebf-e4ea-4309-b7a5-280d10798f36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:23:16,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd4e5ebf-e4ea-4309-b7a5-280d10798f36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:23:16,688] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:23:16,689] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 22:23:16,689] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	81.6424	366	752	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	80.1772	318	752	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	80.1169	346	752	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.6411	222	752	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	78.149	206	752	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	78.1135	204	752	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.938	145	752	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	77.8976	115	752	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.6737	124	752	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 22:23:16,691] [INFO] DFAST Taxonomy check result was written to GCA_019115265.1_ASM1911526v1_genomic.fna/tc_result.tsv
[2023-06-30 22:23:16,692] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:23:16,692] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:23:16,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd4e5ebf-e4ea-4309-b7a5-280d10798f36/dqc_reference/checkm_data
[2023-06-30 22:23:16,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:23:16,726] [INFO] Task started: CheckM
[2023-06-30 22:23:16,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019115265.1_ASM1911526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019115265.1_ASM1911526v1_genomic.fna/checkm_input GCA_019115265.1_ASM1911526v1_genomic.fna/checkm_result
[2023-06-30 22:23:42,931] [INFO] Task succeeded: CheckM
[2023-06-30 22:23:42,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 22:23:42,953] [INFO] ===== Completeness check finished =====
[2023-06-30 22:23:42,954] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:23:42,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019115265.1_ASM1911526v1_genomic.fna/markers.fasta)
[2023-06-30 22:23:42,954] [INFO] Task started: Blastn
[2023-06-30 22:23:42,955] [INFO] Running command: blastn -query GCA_019115265.1_ASM1911526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd4e5ebf-e4ea-4309-b7a5-280d10798f36/dqc_reference/reference_markers_gtdb.fasta -out GCA_019115265.1_ASM1911526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:23:43,829] [INFO] Task succeeded: Blastn
[2023-06-30 22:23:43,834] [INFO] Selected 17 target genomes.
[2023-06-30 22:23:43,835] [INFO] Target genome list was writen to GCA_019115265.1_ASM1911526v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:23:43,843] [INFO] Task started: fastANI
[2023-06-30 22:23:43,843] [INFO] Running command: fastANI --query /var/lib/cwl/stgeab5e83d-86da-476a-a196-bfb7815f9c13/GCA_019115265.1_ASM1911526v1_genomic.fna.gz --refList GCA_019115265.1_ASM1911526v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019115265.1_ASM1911526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:23:54,065] [INFO] Task succeeded: fastANI
[2023-06-30 22:23:54,080] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 22:23:54,081] [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_019115265.1	s__An92 sp019115265	99.9999	745	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002159175.1	s__An92 sp002159175	85.8617	534	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.91	98.91	0.91	0.91	2	-
GCA_019118925.1	s__An92 sp019118925	82.0976	369	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	99.98	99.98	0.93	0.93	2	-
GCF_900199495.1	s__An92 sp900199495	81.5077	378	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.28	97.84	0.85	0.79	7	-
GCF_002161215.1	s__Flavonifractor avistercoris	80.9956	375	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCF_002159455.1	s__Flavonifractor sp002159455	80.9893	366	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	97.17	96.82	0.76	0.75	4	-
GCA_018374635.1	s__An92 sp018374635	80.9399	343	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901735.1	s__An92 sp016901735	80.7252	343	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.81	98.81	0.85	0.85	2	-
GCF_900626285.1	s__Flavonifractor massiliensis_A	80.5459	354	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000239295.1	s__Flavonifractor plautii	80.227	315	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.23	97.77	0.83	0.59	43	-
GCA_019114165.1	s__An92 sp019114165	79.9049	284	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.69	98.69	0.88	0.88	2	-
GCF_009935845.1	s__An92 sp009935845	79.736	331	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161675.1	s__Enterenecus faecium	79.4532	201	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	96.73	96.16	0.87	0.84	6	-
GCF_014287895.1	s__NSJ-51 sp900549795	79.1268	264	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-51	95.0	99.27	99.06	0.90	0.89	3	-
GCA_900553135.1	s__Lawsonibacter sp900553135	79.104	195	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900764755.1	s__Lawsonibacter sp900764755	79.0486	182	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	99.46	99.46	0.86	0.86	2	-
GCA_902363045.1	s__Lawsonibacter sp902363045	78.9953	225	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.07	97.96	0.86	0.80	4	-
--------------------------------------------------------------------------------
[2023-06-30 22:23:54,083] [INFO] GTDB search result was written to GCA_019115265.1_ASM1911526v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:23:54,083] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:23:54,087] [INFO] DFAST_QC result json was written to GCA_019115265.1_ASM1911526v1_genomic.fna/dqc_result.json
[2023-06-30 22:23:54,087] [INFO] DFAST_QC completed!
[2023-06-30 22:23:54,087] [INFO] Total running time: 0h0m53s