[2023-06-13 21:20:33,143] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:20:33,146] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:20:33,146] [INFO] DQC Reference Directory: /var/lib/cwl/stg548a6c11-3a87-47d4-a6ab-276a5e6176f4/dqc_reference
[2023-06-13 21:20:34,304] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:20:34,305] [INFO] Task started: Prodigal
[2023-06-13 21:20:34,305] [INFO] Running command: gunzip -c /var/lib/cwl/stg988161f5-e593-422d-a072-426d296ea70b/GCA_022821985.1_ASM2282198v1_genomic.fna.gz | prodigal -d GCA_022821985.1_ASM2282198v1_genomic.fna/cds.fna -a GCA_022821985.1_ASM2282198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:20:44,851] [INFO] Task succeeded: Prodigal
[2023-06-13 21:20:44,851] [INFO] Task started: HMMsearch
[2023-06-13 21:20:44,851] [INFO] Running command: hmmsearch --tblout GCA_022821985.1_ASM2282198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg548a6c11-3a87-47d4-a6ab-276a5e6176f4/dqc_reference/reference_markers.hmm GCA_022821985.1_ASM2282198v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:20:45,042] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:20:45,043] [INFO] Found 6/6 markers.
[2023-06-13 21:20:45,070] [INFO] Query marker FASTA was written to GCA_022821985.1_ASM2282198v1_genomic.fna/markers.fasta
[2023-06-13 21:20:45,070] [INFO] Task started: Blastn
[2023-06-13 21:20:45,070] [INFO] Running command: blastn -query GCA_022821985.1_ASM2282198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg548a6c11-3a87-47d4-a6ab-276a5e6176f4/dqc_reference/reference_markers.fasta -out GCA_022821985.1_ASM2282198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:20:45,813] [INFO] Task succeeded: Blastn
[2023-06-13 21:20:45,817] [INFO] Selected 28 target genomes.
[2023-06-13 21:20:45,817] [INFO] Target genome list was writen to GCA_022821985.1_ASM2282198v1_genomic.fna/target_genomes.txt
[2023-06-13 21:20:45,821] [INFO] Task started: fastANI
[2023-06-13 21:20:45,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg988161f5-e593-422d-a072-426d296ea70b/GCA_022821985.1_ASM2282198v1_genomic.fna.gz --refList GCA_022821985.1_ASM2282198v1_genomic.fna/target_genomes.txt --output GCA_022821985.1_ASM2282198v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:21:07,669] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:07,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg548a6c11-3a87-47d4-a6ab-276a5e6176f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:21:07,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg548a6c11-3a87-47d4-a6ab-276a5e6176f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:21:07,685] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:21:07,685] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 21:21:07,685] [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
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	77.1584	96	1088	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.884	143	1088	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.5494	87	1088	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.3533	156	1088	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.2937	137	1088	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.248	161	1088	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	75.7087	71	1088	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	75.5161	114	1088	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	75.4497	86	1088	95	below_threshold
Kineosporia corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	75.3971	112	1088	95	below_threshold
Raineyella fluvialis	strain=CBA3103	GCA_009646095.1	2662261	2662261	type	True	75.3933	56	1088	95	below_threshold
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	75.3562	102	1088	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	75.345	54	1088	95	below_threshold
Amycolatopsis dendrobii	strain=DR6-1	GCA_014145675.1	2760662	2760662	type	True	75.3383	103	1088	95	below_threshold
Amycolatopsis rubida	strain=DSM 44637	GCA_900115345.1	112413	112413	type	True	75.3217	116	1088	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	75.307	68	1088	95	below_threshold
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	75.2306	120	1088	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	75.1867	113	1088	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	75.1461	121	1088	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	75.0946	51	1088	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	75.0152	60	1088	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:21:07,688] [INFO] DFAST Taxonomy check result was written to GCA_022821985.1_ASM2282198v1_genomic.fna/tc_result.tsv
[2023-06-13 21:21:07,688] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:21:07,688] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:21:07,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg548a6c11-3a87-47d4-a6ab-276a5e6176f4/dqc_reference/checkm_data
[2023-06-13 21:21:07,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:21:07,721] [INFO] Task started: CheckM
[2023-06-13 21:21:07,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022821985.1_ASM2282198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022821985.1_ASM2282198v1_genomic.fna/checkm_input GCA_022821985.1_ASM2282198v1_genomic.fna/checkm_result
[2023-06-13 21:21:42,920] [INFO] Task succeeded: CheckM
[2023-06-13 21:21:42,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:21:42,944] [INFO] ===== Completeness check finished =====
[2023-06-13 21:21:42,944] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:21:42,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022821985.1_ASM2282198v1_genomic.fna/markers.fasta)
[2023-06-13 21:21:42,945] [INFO] Task started: Blastn
[2023-06-13 21:21:42,945] [INFO] Running command: blastn -query GCA_022821985.1_ASM2282198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg548a6c11-3a87-47d4-a6ab-276a5e6176f4/dqc_reference/reference_markers_gtdb.fasta -out GCA_022821985.1_ASM2282198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:21:44,068] [INFO] Task succeeded: Blastn
[2023-06-13 21:21:44,072] [INFO] Selected 20 target genomes.
[2023-06-13 21:21:44,072] [INFO] Target genome list was writen to GCA_022821985.1_ASM2282198v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:21:44,078] [INFO] Task started: fastANI
[2023-06-13 21:21:44,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg988161f5-e593-422d-a072-426d296ea70b/GCA_022821985.1_ASM2282198v1_genomic.fna.gz --refList GCA_022821985.1_ASM2282198v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022821985.1_ASM2282198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:21:54,691] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:54,706] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 21:21:54,707] [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_009843525.1	s__WTFX01 sp009843525	89.9935	855	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__WTFX01	95.0	98.04	97.52	0.89	0.86	18	-
GCA_011523825.1	s__WTFX01 sp011523825	88.017	814	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__WTFX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051915.1	s__DRKF01 sp011051915	76.7789	124	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__DRKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882825.1	s__F1-20-MAGs160 sp018882825	76.7174	79	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969405.1	s__F1-20-MAGs160 sp018969405	76.6292	104	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781135.1	s__LC5-5 sp016781135	76.5668	86	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__LC5-5	95.0	99.16	98.25	0.93	0.85	8	-
GCA_003697065.1	s__J010 sp003697065	76.4433	116	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	76.3721	176	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.3322	114	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_003962875.1	s__AWTP1-35 sp003962875	76.2902	112	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268735.1	s__AWTP1-35 sp018268735	76.2727	73	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	76.2533	162	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888395.1	s__AC-25 sp005888395	76.1916	97	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-25;g__AC-25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805655.1	s__CADCTF01 sp902805655	76.1049	93	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCTF01;g__CADCTF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845585.1	s__UBA11606 sp016845585	75.9673	133	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936035.1	s__ZC4RG19 sp016936035	75.8718	95	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883045.1	s__RAAP-2 sp017883045	75.8348	62	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238065.1	s__JABABU01 sp014238065	75.7674	98	1088	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__JABABU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 21:21:54,709] [INFO] GTDB search result was written to GCA_022821985.1_ASM2282198v1_genomic.fna/result_gtdb.tsv
[2023-06-13 21:21:54,710] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:21:54,715] [INFO] DFAST_QC result json was written to GCA_022821985.1_ASM2282198v1_genomic.fna/dqc_result.json
[2023-06-13 21:21:54,715] [INFO] DFAST_QC completed!
[2023-06-13 21:21:54,716] [INFO] Total running time: 0h1m22s