[2023-06-30 18:39:30,124] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:39:30,126] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:39:30,127] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bcc2e10-995c-445e-9eda-3ecb676ee44b/dqc_reference
[2023-06-30 18:39:31,311] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:39:31,312] [INFO] Task started: Prodigal
[2023-06-30 18:39:31,312] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ebbd958-9c16-4748-a3aa-dd38f8650e2b/GCA_016795185.1_ASM1679518v1_genomic.fna.gz | prodigal -d GCA_016795185.1_ASM1679518v1_genomic.fna/cds.fna -a GCA_016795185.1_ASM1679518v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:39:54,390] [INFO] Task succeeded: Prodigal
[2023-06-30 18:39:54,391] [INFO] Task started: HMMsearch
[2023-06-30 18:39:54,391] [INFO] Running command: hmmsearch --tblout GCA_016795185.1_ASM1679518v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bcc2e10-995c-445e-9eda-3ecb676ee44b/dqc_reference/reference_markers.hmm GCA_016795185.1_ASM1679518v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:39:54,829] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:39:54,830] [INFO] Found 6/6 markers.
[2023-06-30 18:39:54,906] [INFO] Query marker FASTA was written to GCA_016795185.1_ASM1679518v1_genomic.fna/markers.fasta
[2023-06-30 18:39:54,907] [INFO] Task started: Blastn
[2023-06-30 18:39:54,907] [INFO] Running command: blastn -query GCA_016795185.1_ASM1679518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bcc2e10-995c-445e-9eda-3ecb676ee44b/dqc_reference/reference_markers.fasta -out GCA_016795185.1_ASM1679518v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:39:55,541] [INFO] Task succeeded: Blastn
[2023-06-30 18:39:55,546] [INFO] Selected 30 target genomes.
[2023-06-30 18:39:55,547] [INFO] Target genome list was writen to GCA_016795185.1_ASM1679518v1_genomic.fna/target_genomes.txt
[2023-06-30 18:39:55,549] [INFO] Task started: fastANI
[2023-06-30 18:39:55,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ebbd958-9c16-4748-a3aa-dd38f8650e2b/GCA_016795185.1_ASM1679518v1_genomic.fna.gz --refList GCA_016795185.1_ASM1679518v1_genomic.fna/target_genomes.txt --output GCA_016795185.1_ASM1679518v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:40:25,980] [INFO] Task succeeded: fastANI
[2023-06-30 18:40:25,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bcc2e10-995c-445e-9eda-3ecb676ee44b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:40:25,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bcc2e10-995c-445e-9eda-3ecb676ee44b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:40:26,000] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 18:40:26,000] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 18:40:26,000] [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
Urbifossiella limnaea	strain=ETA_A1	GCA_007747215.1	2528023	2528023	type	True	75.946	342	2384	95	below_threshold
Limnoglobus roseus	strain=PX52	GCA_008254045.1	2598579	2598579	type	True	75.817	253	2384	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.7304	195	2384	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	75.6808	197	2384	95	below_threshold
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	75.6628	211	2384	95	below_threshold
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	75.6246	230	2384	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.6002	117	2384	95	below_threshold
Fimbriiglobus ruber	strain=SP5	GCA_002197845.1	1908690	1908690	type	True	75.5963	195	2384	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.5333	203	2384	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	75.4387	167	2384	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	75.4137	163	2384	95	below_threshold
Zavarzinella formosa	strain=DSM 19928	GCA_000255705.1	360055	360055	type	True	75.4041	130	2384	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.3436	206	2384	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	74.8319	109	2384	95	below_threshold
Devosia enhydra	strain=ATCC 23634	GCA_900119845.1	665118	665118	type	True	74.794	58	2384	95	below_threshold
Nocardia barduliensis	strain=335427	GCA_013315795.1	2736643	2736643	type	True	74.7486	129	2384	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	74.7483	195	2384	95	below_threshold
Herbidospora solisilvae	strain=NEAU-GS84	GCA_009901565.1	2696284	2696284	type	True	74.7394	180	2384	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	74.7265	126	2384	95	below_threshold
Acrocarpospora phusangensis	strain=NBRC 108782	GCA_016862995.1	1070424	1070424	type	True	74.7119	172	2384	95	below_threshold
Nocardiopsis algeriensis	strain=CECT 8712	GCA_014203695.1	1478215	1478215	type	True	74.6832	66	2384	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	74.6031	136	2384	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	74.5812	172	2384	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 18:40:26,002] [INFO] DFAST Taxonomy check result was written to GCA_016795185.1_ASM1679518v1_genomic.fna/tc_result.tsv
[2023-06-30 18:40:26,003] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:40:26,003] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:40:26,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bcc2e10-995c-445e-9eda-3ecb676ee44b/dqc_reference/checkm_data
[2023-06-30 18:40:26,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:40:26,092] [INFO] Task started: CheckM
[2023-06-30 18:40:26,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016795185.1_ASM1679518v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016795185.1_ASM1679518v1_genomic.fna/checkm_input GCA_016795185.1_ASM1679518v1_genomic.fna/checkm_result
[2023-06-30 18:41:31,841] [INFO] Task succeeded: CheckM
[2023-06-30 18:41:31,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 18:41:31,869] [INFO] ===== Completeness check finished =====
[2023-06-30 18:41:31,869] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:41:31,869] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016795185.1_ASM1679518v1_genomic.fna/markers.fasta)
[2023-06-30 18:41:31,869] [INFO] Task started: Blastn
[2023-06-30 18:41:31,870] [INFO] Running command: blastn -query GCA_016795185.1_ASM1679518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bcc2e10-995c-445e-9eda-3ecb676ee44b/dqc_reference/reference_markers_gtdb.fasta -out GCA_016795185.1_ASM1679518v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:41:32,762] [INFO] Task succeeded: Blastn
[2023-06-30 18:41:32,767] [INFO] Selected 26 target genomes.
[2023-06-30 18:41:32,767] [INFO] Target genome list was writen to GCA_016795185.1_ASM1679518v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:41:32,771] [INFO] Task started: fastANI
[2023-06-30 18:41:32,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ebbd958-9c16-4748-a3aa-dd38f8650e2b/GCA_016795185.1_ASM1679518v1_genomic.fna.gz --refList GCA_016795185.1_ASM1679518v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016795185.1_ASM1679518v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:41:58,374] [INFO] Task succeeded: fastANI
[2023-06-30 18:41:58,392] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 18:41:58,392] [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_016873095.1	s__VGYC01 sp016873095	76.5039	342	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__VGYC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016177925.1	s__JACOUH01 sp016177925	76.1852	329	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__JACOUH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002404095.1	s__UBA4732 sp002404095	76.0985	246	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA4732	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200155.1	s__SIAQ01 sp016200155	76.0472	214	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191165.1	s__SIAQ01 sp016191165	76.0404	213	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692065.1	s__SIAQ01 sp009692065	75.9783	243	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195405.1	s__JACPZP01 sp016195405	75.9516	209	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__JACPZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823135.1	s__Gemmata sp013823135	75.9073	149	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872605.1	s__SIAQ01 sp016872605	75.8246	206	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872595.1	s__Gemmata sp016872595	75.783	286	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331615.1	s__DSRJ01 sp011331615	75.7297	142	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__DSRJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005799265.1	s__SIAQ01 sp005799265	75.7046	213	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01	95.0	99.88	99.81	0.92	0.91	3	-
GCA_017308215.1	s__Urbifossiella sp017308215	75.6995	312	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956985.1	s__Paludisphaera borealis	75.6741	200	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065095.1	s__Gemmata obscuriglobus	75.6238	230	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.98	99.95	1.00	1.00	4	-
GCA_019237095.1	s__JAFAHT01 sp019237095	75.4807	76	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__JAFAHT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977685.1	s__Tautonia sociabilis	75.4291	169	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011065895.1	s__Paludisphaera sp011065895	75.4137	163	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671185.1	s__QWPN01 sp003671185	75.3789	61	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610835.1	s__Planctomyces_A sp001610835	75.3371	116	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242475.1	s__QHXN01 sp019242475	74.9658	110	2384	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515235.1	s__Anammoximicrobium sp012515235	74.9482	127	2384	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Anammoximicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526565.1	s__WYBL01 sp011526565	74.8235	168	2384	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Fen-336;f__Fen-336;g__WYBL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 18:41:58,395] [INFO] GTDB search result was written to GCA_016795185.1_ASM1679518v1_genomic.fna/result_gtdb.tsv
[2023-06-30 18:41:58,395] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:41:58,400] [INFO] DFAST_QC result json was written to GCA_016795185.1_ASM1679518v1_genomic.fna/dqc_result.json
[2023-06-30 18:41:58,401] [INFO] DFAST_QC completed!
[2023-06-30 18:41:58,401] [INFO] Total running time: 0h2m28s