[2023-06-29 16:38:52,412] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:38:52,415] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:38:52,415] [INFO] DQC Reference Directory: /var/lib/cwl/stge15700a6-bfaf-4984-912d-c7de7ae1af36/dqc_reference
[2023-06-29 16:38:53,788] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:38:53,789] [INFO] Task started: Prodigal
[2023-06-29 16:38:53,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg67adaad7-c266-4048-b6fe-a64b8b619ab1/GCA_011053145.1_ASM1105314v1_genomic.fna.gz | prodigal -d GCA_011053145.1_ASM1105314v1_genomic.fna/cds.fna -a GCA_011053145.1_ASM1105314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:39:03,191] [INFO] Task succeeded: Prodigal
[2023-06-29 16:39:03,191] [INFO] Task started: HMMsearch
[2023-06-29 16:39:03,191] [INFO] Running command: hmmsearch --tblout GCA_011053145.1_ASM1105314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge15700a6-bfaf-4984-912d-c7de7ae1af36/dqc_reference/reference_markers.hmm GCA_011053145.1_ASM1105314v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:39:03,458] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:39:03,464] [INFO] Found 6/6 markers.
[2023-06-29 16:39:03,514] [INFO] Query marker FASTA was written to GCA_011053145.1_ASM1105314v1_genomic.fna/markers.fasta
[2023-06-29 16:39:03,515] [INFO] Task started: Blastn
[2023-06-29 16:39:03,515] [INFO] Running command: blastn -query GCA_011053145.1_ASM1105314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge15700a6-bfaf-4984-912d-c7de7ae1af36/dqc_reference/reference_markers.fasta -out GCA_011053145.1_ASM1105314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:39:04,323] [INFO] Task succeeded: Blastn
[2023-06-29 16:39:04,328] [INFO] Selected 29 target genomes.
[2023-06-29 16:39:04,328] [INFO] Target genome list was writen to GCA_011053145.1_ASM1105314v1_genomic.fna/target_genomes.txt
[2023-06-29 16:39:04,331] [INFO] Task started: fastANI
[2023-06-29 16:39:04,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg67adaad7-c266-4048-b6fe-a64b8b619ab1/GCA_011053145.1_ASM1105314v1_genomic.fna.gz --refList GCA_011053145.1_ASM1105314v1_genomic.fna/target_genomes.txt --output GCA_011053145.1_ASM1105314v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:39:26,651] [INFO] Task succeeded: fastANI
[2023-06-29 16:39:26,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge15700a6-bfaf-4984-912d-c7de7ae1af36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:39:26,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge15700a6-bfaf-4984-912d-c7de7ae1af36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:39:26,666] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:39:26,666] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:39:26,666] [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
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.9883	88	1154	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	74.9506	70	1154	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	74.9396	56	1154	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	74.9378	72	1154	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.9114	94	1154	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	74.7899	55	1154	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	74.7884	54	1154	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	74.7863	55	1154	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.776	67	1154	95	below_threshold
Actinoplanes globisporus	strain=DSM 43857	GCA_000379645.1	113565	113565	type	True	74.756	84	1154	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	74.7477	73	1154	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	74.7337	76	1154	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.6943	100	1154	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	74.6894	78	1154	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	74.662	76	1154	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:39:26,668] [INFO] DFAST Taxonomy check result was written to GCA_011053145.1_ASM1105314v1_genomic.fna/tc_result.tsv
[2023-06-29 16:39:26,669] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:39:26,669] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:39:26,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge15700a6-bfaf-4984-912d-c7de7ae1af36/dqc_reference/checkm_data
[2023-06-29 16:39:26,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:39:26,712] [INFO] Task started: CheckM
[2023-06-29 16:39:26,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011053145.1_ASM1105314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011053145.1_ASM1105314v1_genomic.fna/checkm_input GCA_011053145.1_ASM1105314v1_genomic.fna/checkm_result
[2023-06-29 16:39:58,195] [INFO] Task succeeded: CheckM
[2023-06-29 16:39:58,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:39:58,221] [INFO] ===== Completeness check finished =====
[2023-06-29 16:39:58,221] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:39:58,221] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011053145.1_ASM1105314v1_genomic.fna/markers.fasta)
[2023-06-29 16:39:58,222] [INFO] Task started: Blastn
[2023-06-29 16:39:58,222] [INFO] Running command: blastn -query GCA_011053145.1_ASM1105314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge15700a6-bfaf-4984-912d-c7de7ae1af36/dqc_reference/reference_markers_gtdb.fasta -out GCA_011053145.1_ASM1105314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:39:59,478] [INFO] Task succeeded: Blastn
[2023-06-29 16:39:59,483] [INFO] Selected 22 target genomes.
[2023-06-29 16:39:59,483] [INFO] Target genome list was writen to GCA_011053145.1_ASM1105314v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:39:59,496] [INFO] Task started: fastANI
[2023-06-29 16:39:59,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg67adaad7-c266-4048-b6fe-a64b8b619ab1/GCA_011053145.1_ASM1105314v1_genomic.fna.gz --refList GCA_011053145.1_ASM1105314v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011053145.1_ASM1105314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:40:14,509] [INFO] Task succeeded: fastANI
[2023-06-29 16:40:14,527] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:40:14,527] [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_011053145.1	s__DRLC01 sp011053145	100.0	1135	1154	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__DRLC01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013140785.1	s__JABFRZ01 sp013140785	76.936	167	1154	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826945.1	s__RBC036 sp902826945	76.9155	285	1154	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RBC036	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691855.1	s__JABFRZ01 sp009691855	76.8512	202	1154	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125265.1	s__RI-242 sp016125265	76.5903	142	1154	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RI-242	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872755.1	s__GW928-bin9 sp016872755	76.5732	158	1154	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007750655.1	s__Pla163 sp007750655	76.5028	179	1154	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525785.1	s__WYBT01 sp011525785	76.2968	192	1154	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	76.2474	152	1154	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296785.1	s__GW928-bin9 sp004296785	76.1856	146	1154	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016220085.1	s__JACRIN01 sp016220085	76.0496	191	1154	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JACRIN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016220035.1	s__JADJNY01 sp016220035	75.9782	199	1154	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017569225.1	s__Cellulomonas sp017569225	74.8457	63	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306785.1	s__Modestobacter marinus_A	74.7689	64	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143215.1	s__Geodermatophilus obscurus_A	74.7664	64	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:40:14,529] [INFO] GTDB search result was written to GCA_011053145.1_ASM1105314v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:40:14,530] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:40:14,534] [INFO] DFAST_QC result json was written to GCA_011053145.1_ASM1105314v1_genomic.fna/dqc_result.json
[2023-06-29 16:40:14,534] [INFO] DFAST_QC completed!
[2023-06-29 16:40:14,534] [INFO] Total running time: 0h1m22s