[2023-07-01 05:18:01,925] [INFO] DFAST_QC pipeline started.
[2023-07-01 05:18:01,927] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 05:18:01,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg86cf9e67-4268-42d5-8cb5-d6aa361b0261/dqc_reference
[2023-07-01 05:18:03,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 05:18:03,309] [INFO] Task started: Prodigal
[2023-07-01 05:18:03,309] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1bf6d7c-6923-48c9-8098-4575522ed20d/GCA_019233655.1_ASM1923365v1_genomic.fna.gz | prodigal -d GCA_019233655.1_ASM1923365v1_genomic.fna/cds.fna -a GCA_019233655.1_ASM1923365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 05:18:06,916] [INFO] Task succeeded: Prodigal
[2023-07-01 05:18:06,916] [INFO] Task started: HMMsearch
[2023-07-01 05:18:06,916] [INFO] Running command: hmmsearch --tblout GCA_019233655.1_ASM1923365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86cf9e67-4268-42d5-8cb5-d6aa361b0261/dqc_reference/reference_markers.hmm GCA_019233655.1_ASM1923365v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 05:18:07,073] [INFO] Task succeeded: HMMsearch
[2023-07-01 05:18:07,074] [INFO] Found 6/6 markers.
[2023-07-01 05:18:07,096] [INFO] Query marker FASTA was written to GCA_019233655.1_ASM1923365v1_genomic.fna/markers.fasta
[2023-07-01 05:18:07,096] [INFO] Task started: Blastn
[2023-07-01 05:18:07,096] [INFO] Running command: blastn -query GCA_019233655.1_ASM1923365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86cf9e67-4268-42d5-8cb5-d6aa361b0261/dqc_reference/reference_markers.fasta -out GCA_019233655.1_ASM1923365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:18:08,367] [INFO] Task succeeded: Blastn
[2023-07-01 05:18:08,371] [INFO] Selected 22 target genomes.
[2023-07-01 05:18:08,371] [INFO] Target genome list was writen to GCA_019233655.1_ASM1923365v1_genomic.fna/target_genomes.txt
[2023-07-01 05:18:08,372] [INFO] Task started: fastANI
[2023-07-01 05:18:08,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1bf6d7c-6923-48c9-8098-4575522ed20d/GCA_019233655.1_ASM1923365v1_genomic.fna.gz --refList GCA_019233655.1_ASM1923365v1_genomic.fna/target_genomes.txt --output GCA_019233655.1_ASM1923365v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 05:18:26,480] [INFO] Task succeeded: fastANI
[2023-07-01 05:18:26,480] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86cf9e67-4268-42d5-8cb5-d6aa361b0261/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 05:18:26,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86cf9e67-4268-42d5-8cb5-d6aa361b0261/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 05:18:26,497] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 05:18:26,497] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 05:18:26,497] [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
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	78.4532	267	489	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	76.202	250	489	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	76.0063	244	489	95	below_threshold
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	75.9866	148	489	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.9832	186	489	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	75.9602	206	489	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	75.8194	159	489	95	below_threshold
Phytohabitans flavus	strain=NBRC 107702	GCA_011764545.1	1076124	1076124	type	True	75.2811	137	489	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	75.2028	105	489	95	below_threshold
Frankia canadensis		GCA_900197875.1	1836972	1836972	type	True	75.1896	103	489	95	below_threshold
Modestobacter caceresii	strain=KNN 45-2b	GCA_000761485.1	1522368	1522368	type	True	75.187	86	489	95	below_threshold
Nakamurella leprariae	strain=YIM 132084	GCA_016918035.1	2803911	2803911	type	True	75.1591	68	489	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	75.1202	98	489	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	75.0835	150	489	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	75.0413	67	489	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	75.009	169	489	95	below_threshold
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	74.9837	111	489	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	74.9731	71	489	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	74.9215	148	489	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	74.7077	51	489	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 05:18:26,499] [INFO] DFAST Taxonomy check result was written to GCA_019233655.1_ASM1923365v1_genomic.fna/tc_result.tsv
[2023-07-01 05:18:26,499] [INFO] ===== Taxonomy check completed =====
[2023-07-01 05:18:26,500] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 05:18:26,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86cf9e67-4268-42d5-8cb5-d6aa361b0261/dqc_reference/checkm_data
[2023-07-01 05:18:26,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 05:18:26,524] [INFO] Task started: CheckM
[2023-07-01 05:18:26,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019233655.1_ASM1923365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019233655.1_ASM1923365v1_genomic.fna/checkm_input GCA_019233655.1_ASM1923365v1_genomic.fna/checkm_result
[2023-07-01 05:18:48,365] [INFO] Task succeeded: CheckM
[2023-07-01 05:18:48,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.47%
Contamintation: 8.85%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-07-01 05:18:48,385] [INFO] ===== Completeness check finished =====
[2023-07-01 05:18:48,385] [INFO] ===== Start GTDB Search =====
[2023-07-01 05:18:48,385] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019233655.1_ASM1923365v1_genomic.fna/markers.fasta)
[2023-07-01 05:18:48,386] [INFO] Task started: Blastn
[2023-07-01 05:18:48,386] [INFO] Running command: blastn -query GCA_019233655.1_ASM1923365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86cf9e67-4268-42d5-8cb5-d6aa361b0261/dqc_reference/reference_markers_gtdb.fasta -out GCA_019233655.1_ASM1923365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:18:49,653] [INFO] Task succeeded: Blastn
[2023-07-01 05:18:49,657] [INFO] Selected 18 target genomes.
[2023-07-01 05:18:49,657] [INFO] Target genome list was writen to GCA_019233655.1_ASM1923365v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 05:18:49,659] [INFO] Task started: fastANI
[2023-07-01 05:18:49,659] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1bf6d7c-6923-48c9-8098-4575522ed20d/GCA_019233655.1_ASM1923365v1_genomic.fna.gz --refList GCA_019233655.1_ASM1923365v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019233655.1_ASM1923365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 05:18:58,587] [INFO] Task succeeded: fastANI
[2023-07-01 05:18:58,601] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 05:18:58,602] [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_019236545.1	s__Palsa-739 sp019236545	98.1889	401	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	98.19	98.19	0.82	0.82	2	conclusive
GCA_003161615.1	s__Palsa-739 sp003161615	82.0712	294	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883365.1	s__Palsa-739 sp005883365	81.4174	255	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003139545.1	s__Palsa-739 sp003139545	81.1073	329	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019234175.1	s__Palsa-739 sp019234175	81.051	238	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884575.1	s__AC-16 sp005884575	80.3587	348	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003152275.1	s__Palsa-739 sp003152275	79.8683	296	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	96.63	96.63	0.81	0.81	2	-
GCA_005885565.1	s__AC-50 sp005885565	79.2166	255	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-50	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812235.1	s__JACCTU01 sp013812235	78.8448	154	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883335.1	s__AC-32 sp005883335	78.8074	220	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883235.1	s__AC-50 sp005883235	78.6561	162	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-50	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362295.1	s__PALSA-600 sp013362295	78.6371	246	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__PALSA-600	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005885085.1	s__3-1-20CM-4-69-9 sp005885085	78.4693	206	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__3-1-20CM-4-69-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884155.1	s__AC-32 sp005884155	78.3604	195	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014534295.1	s__JACVRU01 sp014534295	78.2533	161	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACVRU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697275.1	s__JACVSB01 sp013697275	78.0246	150	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACVSB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014534345.1	s__JACVRR01 sp014534345	77.5704	192	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACVRR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888335.1	s__VAWY01 sp005888335	76.679	234	489	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__VAWY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 05:18:58,603] [INFO] GTDB search result was written to GCA_019233655.1_ASM1923365v1_genomic.fna/result_gtdb.tsv
[2023-07-01 05:18:58,604] [INFO] ===== GTDB Search completed =====
[2023-07-01 05:18:58,608] [INFO] DFAST_QC result json was written to GCA_019233655.1_ASM1923365v1_genomic.fna/dqc_result.json
[2023-07-01 05:18:58,608] [INFO] DFAST_QC completed!
[2023-07-01 05:18:58,608] [INFO] Total running time: 0h0m57s