[2023-06-30 03:29:18,946] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:29:18,949] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:29:18,950] [INFO] DQC Reference Directory: /var/lib/cwl/stg5286f079-786f-465b-9dc0-3cd09a134596/dqc_reference
[2023-06-30 03:29:20,484] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:29:20,485] [INFO] Task started: Prodigal
[2023-06-30 03:29:20,485] [INFO] Running command: gunzip -c /var/lib/cwl/stgf353c0fc-a7a2-4752-babd-ef8fb3e13b1a/GCA_016794765.1_ASM1679476v1_genomic.fna.gz | prodigal -d GCA_016794765.1_ASM1679476v1_genomic.fna/cds.fna -a GCA_016794765.1_ASM1679476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:29:27,608] [INFO] Task succeeded: Prodigal
[2023-06-30 03:29:27,609] [INFO] Task started: HMMsearch
[2023-06-30 03:29:27,609] [INFO] Running command: hmmsearch --tblout GCA_016794765.1_ASM1679476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5286f079-786f-465b-9dc0-3cd09a134596/dqc_reference/reference_markers.hmm GCA_016794765.1_ASM1679476v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:29:27,869] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:29:27,870] [INFO] Found 6/6 markers.
[2023-06-30 03:29:27,904] [INFO] Query marker FASTA was written to GCA_016794765.1_ASM1679476v1_genomic.fna/markers.fasta
[2023-06-30 03:29:27,905] [INFO] Task started: Blastn
[2023-06-30 03:29:27,905] [INFO] Running command: blastn -query GCA_016794765.1_ASM1679476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5286f079-786f-465b-9dc0-3cd09a134596/dqc_reference/reference_markers.fasta -out GCA_016794765.1_ASM1679476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:29:28,575] [INFO] Task succeeded: Blastn
[2023-06-30 03:29:28,579] [INFO] Selected 31 target genomes.
[2023-06-30 03:29:28,580] [INFO] Target genome list was writen to GCA_016794765.1_ASM1679476v1_genomic.fna/target_genomes.txt
[2023-06-30 03:29:28,591] [INFO] Task started: fastANI
[2023-06-30 03:29:28,591] [INFO] Running command: fastANI --query /var/lib/cwl/stgf353c0fc-a7a2-4752-babd-ef8fb3e13b1a/GCA_016794765.1_ASM1679476v1_genomic.fna.gz --refList GCA_016794765.1_ASM1679476v1_genomic.fna/target_genomes.txt --output GCA_016794765.1_ASM1679476v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:29:55,604] [INFO] Task succeeded: fastANI
[2023-06-30 03:29:55,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5286f079-786f-465b-9dc0-3cd09a134596/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:29:55,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5286f079-786f-465b-9dc0-3cd09a134596/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:29:55,626] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:29:55,627] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:29:55,627] [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
Geothrix fermentans	strain=DSM 14018	GCA_000428885.1	44676	44676	type	True	75.2868	54	891	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.1468	90	891	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	75.0726	63	891	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	74.9657	69	891	95	below_threshold
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	74.9195	59	891	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	74.771	129	891	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	74.7503	60	891	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	74.7409	181	891	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	74.7284	110	891	95	below_threshold
Streptomyces longispororuber	strain=JCM 4784	GCA_014656095.1	68230	68230	type	True	74.7265	164	891	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	74.7207	83	891	95	below_threshold
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	74.6585	98	891	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001558125.2	546365	546365	type	True	74.6555	76	891	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001613935.1	546365	546365	type	True	74.6522	80	891	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	74.6127	86	891	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:29:55,629] [INFO] DFAST Taxonomy check result was written to GCA_016794765.1_ASM1679476v1_genomic.fna/tc_result.tsv
[2023-06-30 03:29:55,630] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:29:55,630] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:29:55,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5286f079-786f-465b-9dc0-3cd09a134596/dqc_reference/checkm_data
[2023-06-30 03:29:55,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:29:55,669] [INFO] Task started: CheckM
[2023-06-30 03:29:55,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016794765.1_ASM1679476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016794765.1_ASM1679476v1_genomic.fna/checkm_input GCA_016794765.1_ASM1679476v1_genomic.fna/checkm_result
[2023-06-30 03:30:21,459] [INFO] Task succeeded: CheckM
[2023-06-30 03:30:21,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:30:21,481] [INFO] ===== Completeness check finished =====
[2023-06-30 03:30:21,482] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:30:21,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016794765.1_ASM1679476v1_genomic.fna/markers.fasta)
[2023-06-30 03:30:21,482] [INFO] Task started: Blastn
[2023-06-30 03:30:21,483] [INFO] Running command: blastn -query GCA_016794765.1_ASM1679476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5286f079-786f-465b-9dc0-3cd09a134596/dqc_reference/reference_markers_gtdb.fasta -out GCA_016794765.1_ASM1679476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:30:22,479] [INFO] Task succeeded: Blastn
[2023-06-30 03:30:22,484] [INFO] Selected 17 target genomes.
[2023-06-30 03:30:22,484] [INFO] Target genome list was writen to GCA_016794765.1_ASM1679476v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:30:22,488] [INFO] Task started: fastANI
[2023-06-30 03:30:22,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgf353c0fc-a7a2-4752-babd-ef8fb3e13b1a/GCA_016794765.1_ASM1679476v1_genomic.fna.gz --refList GCA_016794765.1_ASM1679476v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016794765.1_ASM1679476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:30:31,478] [INFO] Task succeeded: fastANI
[2023-06-30 03:30:31,500] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:30:31,500] [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_016794765.1	s__JAEUJG01 sp016794765	100.0	873	891	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__JAEUJG01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018262985.1	s__JAFGNN01 sp018262985	78.3916	278	891	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__JAFGNN01	95.0	98.32	98.32	0.96	0.96	2	-
GCA_016926955.1	s__JAFGNN01 sp016926955	78.1397	236	891	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__JAFGNN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002307245.1	s__UBA1306 sp002307245	78.1222	268	891	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__UBA1306	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003247225.1	s__SZUA-370 sp003247225	77.8869	228	891	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__SZUA-370	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821875.1	s__CAIJMU01 sp903821875	77.4814	172	891	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__CAIJMU01	95.0	99.44	98.70	0.93	0.88	8	-
GCA_002839315.1	s__SZUA-370 sp002839315	77.4762	164	891	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__SZUA-370	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018816345.1	s__SZUA-370 sp018816345	77.3461	202	891	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__SZUA-370	95.0	99.89	99.89	0.86	0.86	2	-
GCA_012517645.1	s__JAAYUR01 sp012517645	77.2331	127	891	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__JAAYUR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003245635.1	s__SZUA-426 sp003245635	77.1294	95	891	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Termitinemataceae;g__SZUA-426	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002383375.1	s__UBA2256 sp002383375	76.5496	52	891	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__UBA2256	95.0	99.59	99.59	0.92	0.92	2	-
GCA_011525805.1	s__UBA5793 sp011525805	74.8126	58	891	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA5793;g__UBA5793	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 03:30:31,502] [INFO] GTDB search result was written to GCA_016794765.1_ASM1679476v1_genomic.fna/result_gtdb.tsv
[2023-06-30 03:30:31,503] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:30:31,521] [INFO] DFAST_QC result json was written to GCA_016794765.1_ASM1679476v1_genomic.fna/dqc_result.json
[2023-06-30 03:30:31,521] [INFO] DFAST_QC completed!
[2023-06-30 03:30:31,522] [INFO] Total running time: 0h1m13s