[2023-06-08 12:27:15,195] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:27:15,203] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:27:15,204] [INFO] DQC Reference Directory: /var/lib/cwl/stge35daed6-e62d-4540-8f6e-64cab0a2d78b/dqc_reference
[2023-06-08 12:27:16,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:27:16,420] [INFO] Task started: Prodigal
[2023-06-08 12:27:16,420] [INFO] Running command: gunzip -c /var/lib/cwl/stg4babc13f-7b02-4eab-a4b8-2f63b95ef07d/GCA_947473045.1_RH-23may17-1049_genomic.fna.gz | prodigal -d GCA_947473045.1_RH-23may17-1049_genomic.fna/cds.fna -a GCA_947473045.1_RH-23may17-1049_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:27:30,716] [INFO] Task succeeded: Prodigal
[2023-06-08 12:27:30,716] [INFO] Task started: HMMsearch
[2023-06-08 12:27:30,716] [INFO] Running command: hmmsearch --tblout GCA_947473045.1_RH-23may17-1049_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge35daed6-e62d-4540-8f6e-64cab0a2d78b/dqc_reference/reference_markers.hmm GCA_947473045.1_RH-23may17-1049_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:27:31,019] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:27:31,020] [INFO] Found 6/6 markers.
[2023-06-08 12:27:31,068] [INFO] Query marker FASTA was written to GCA_947473045.1_RH-23may17-1049_genomic.fna/markers.fasta
[2023-06-08 12:27:31,069] [INFO] Task started: Blastn
[2023-06-08 12:27:31,069] [INFO] Running command: blastn -query GCA_947473045.1_RH-23may17-1049_genomic.fna/markers.fasta -db /var/lib/cwl/stge35daed6-e62d-4540-8f6e-64cab0a2d78b/dqc_reference/reference_markers.fasta -out GCA_947473045.1_RH-23may17-1049_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:27:31,759] [INFO] Task succeeded: Blastn
[2023-06-08 12:27:31,763] [INFO] Selected 31 target genomes.
[2023-06-08 12:27:31,764] [INFO] Target genome list was writen to GCA_947473045.1_RH-23may17-1049_genomic.fna/target_genomes.txt
[2023-06-08 12:27:31,772] [INFO] Task started: fastANI
[2023-06-08 12:27:31,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg4babc13f-7b02-4eab-a4b8-2f63b95ef07d/GCA_947473045.1_RH-23may17-1049_genomic.fna.gz --refList GCA_947473045.1_RH-23may17-1049_genomic.fna/target_genomes.txt --output GCA_947473045.1_RH-23may17-1049_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:28:05,655] [INFO] Task succeeded: fastANI
[2023-06-08 12:28:05,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge35daed6-e62d-4540-8f6e-64cab0a2d78b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:28:05,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge35daed6-e62d-4540-8f6e-64cab0a2d78b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:28:05,676] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:28:05,677] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:28:05,677] [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
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	76.2616	410	1650	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.4729	403	1650	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.3787	348	1650	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.3682	360	1650	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	75.32	213	1650	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	75.1262	63	1650	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.8908	156	1650	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.886	157	1650	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	74.8792	100	1650	95	below_threshold
Actinomadura pelletieri	strain=DSM 43383	GCA_003634705.1	111805	111805	type	True	74.8777	98	1650	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	74.8172	126	1650	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	74.8112	83	1650	95	below_threshold
Herbidospora sakaeratensis	strain=NBRC 102641	GCA_001570525.1	564415	564415	type	True	74.7847	125	1650	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	74.7822	80	1650	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	74.7631	97	1650	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	74.7584	151	1650	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	74.7545	136	1650	95	below_threshold
Pseudoclavibacter chungangensis	strain=DSM 23821	GCA_013410545.1	587635	587635	type	True	74.7524	99	1650	95	below_threshold
Pseudoclavibacter chungangensis	strain=DSM 23821	GCA_008831135.1	587635	587635	type	True	74.7508	100	1650	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	74.743	102	1650	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	74.7406	103	1650	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	74.707	134	1650	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	74.7045	125	1650	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	74.7014	114	1650	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	74.6904	78	1650	95	below_threshold
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	74.6494	111	1650	95	below_threshold
Streptomyces fulvorobeus	strain=DSM 41455	GCA_013409565.1	284028	284028	type	True	74.6046	62	1650	95	below_threshold
Streptomyces fulvorobeus	strain=NBRC 15897	GCA_013167895.1	284028	284028	type	True	74.6046	62	1650	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:28:05,682] [INFO] DFAST Taxonomy check result was written to GCA_947473045.1_RH-23may17-1049_genomic.fna/tc_result.tsv
[2023-06-08 12:28:05,682] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:28:05,683] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:28:05,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge35daed6-e62d-4540-8f6e-64cab0a2d78b/dqc_reference/checkm_data
[2023-06-08 12:28:05,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:28:05,742] [INFO] Task started: CheckM
[2023-06-08 12:28:05,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947473045.1_RH-23may17-1049_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947473045.1_RH-23may17-1049_genomic.fna/checkm_input GCA_947473045.1_RH-23may17-1049_genomic.fna/checkm_result
[2023-06-08 12:28:47,900] [INFO] Task succeeded: CheckM
[2023-06-08 12:28:47,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:28:47,925] [INFO] ===== Completeness check finished =====
[2023-06-08 12:28:47,925] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:28:47,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947473045.1_RH-23may17-1049_genomic.fna/markers.fasta)
[2023-06-08 12:28:47,926] [INFO] Task started: Blastn
[2023-06-08 12:28:47,926] [INFO] Running command: blastn -query GCA_947473045.1_RH-23may17-1049_genomic.fna/markers.fasta -db /var/lib/cwl/stge35daed6-e62d-4540-8f6e-64cab0a2d78b/dqc_reference/reference_markers_gtdb.fasta -out GCA_947473045.1_RH-23may17-1049_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:28:48,926] [INFO] Task succeeded: Blastn
[2023-06-08 12:28:48,932] [INFO] Selected 26 target genomes.
[2023-06-08 12:28:48,932] [INFO] Target genome list was writen to GCA_947473045.1_RH-23may17-1049_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:28:49,034] [INFO] Task started: fastANI
[2023-06-08 12:28:49,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg4babc13f-7b02-4eab-a4b8-2f63b95ef07d/GCA_947473045.1_RH-23may17-1049_genomic.fna.gz --refList GCA_947473045.1_RH-23may17-1049_genomic.fna/target_genomes_gtdb.txt --output GCA_947473045.1_RH-23may17-1049_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:29:18,879] [INFO] Task succeeded: fastANI
[2023-06-08 12:29:18,901] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 12:29:18,902] [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_016703425.1	s__JADJCA01 sp016703425	76.4239	320	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JADJCA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712525.1	s__JAAFHV01 sp016712525	76.3218	398	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001263205.1	s__Labilithrix luteola	76.2814	405	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899635.1	s__Labilithrix sp001899635	76.1665	457	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Labilithrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893335.1	s__CAITLX01 sp903893335	76.1591	310	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720545.1	s__JAAFHV01 sp016720545	76.1271	396	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	99.45	99.45	0.94	0.94	2	-
GCA_003151595.1	s__PALSA-1152 sp003151595	76.0953	370	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__PALSA-1152	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153495.1	s__Palsa-1150 sp003153495	76.013	210	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Palsa-1150	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003139415.1	s__Palsa-1150 sp003139415	75.9866	215	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Palsa-1150	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297655.1	s__JAAFHV01 sp013297655	75.8784	357	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906315.1	s__CAIVJW01 sp903906315	75.7924	386	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIVJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005777185.1	s__SXNL01 sp005777185	75.6321	296	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__SXNL01	95.0	99.91	99.91	0.95	0.95	3	-
GCA_013298325.1	s__JAAFHJ01 sp013298325	75.5923	113	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001931535.1	s__Minicystis rosea	75.4929	440	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Minicystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144635.1	s__Polyangium sp005144635	75.4639	404	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881185.1	s__JADGRF01 sp017881185	75.451	117	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JAFGIB01;g__JADGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704445.1	s__SCUS01 sp016704445	75.2828	241	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Ga0077539;g__SCUS01	95.0	98.47	98.28	0.90	0.89	4	-
GCA_016212965.1	s__JACRDA01 sp016212965	75.2251	361	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JACRDA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297725.1	s__SCUS01 sp004297725	75.1853	257	1650	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Ga0077539;g__SCUS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016879935.1	s__JAEUJQ01 sp016879935	75.0746	218	1650	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JAEUJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432485.1	s__Spirillospora sp003432485	74.76	98	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715355.1	s__Agromyces sp006715355	74.6702	122	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:29:18,904] [INFO] GTDB search result was written to GCA_947473045.1_RH-23may17-1049_genomic.fna/result_gtdb.tsv
[2023-06-08 12:29:18,904] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:29:18,909] [INFO] DFAST_QC result json was written to GCA_947473045.1_RH-23may17-1049_genomic.fna/dqc_result.json
[2023-06-08 12:29:18,909] [INFO] DFAST_QC completed!
[2023-06-08 12:29:18,909] [INFO] Total running time: 0h2m4s