[2024-01-24 14:05:34,137] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:34,138] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:34,138] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2e516c7-42a6-434c-a5ce-44d590094379/dqc_reference
[2024-01-24 14:05:35,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,416] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,416] [INFO] Running command: gunzip -c /var/lib/cwl/stg95032d8a-0482-401c-8918-60efd1575728/GCF_030159095.1_ASM3015909v1_genomic.fna.gz | prodigal -d GCF_030159095.1_ASM3015909v1_genomic.fna/cds.fna -a GCF_030159095.1_ASM3015909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:52,410] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:52,411] [INFO] Task started: HMMsearch
[2024-01-24 14:05:52,411] [INFO] Running command: hmmsearch --tblout GCF_030159095.1_ASM3015909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2e516c7-42a6-434c-a5ce-44d590094379/dqc_reference/reference_markers.hmm GCF_030159095.1_ASM3015909v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:52,723] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:52,724] [INFO] Found 6/6 markers.
[2024-01-24 14:05:52,782] [INFO] Query marker FASTA was written to GCF_030159095.1_ASM3015909v1_genomic.fna/markers.fasta
[2024-01-24 14:05:52,782] [INFO] Task started: Blastn
[2024-01-24 14:05:52,782] [INFO] Running command: blastn -query GCF_030159095.1_ASM3015909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2e516c7-42a6-434c-a5ce-44d590094379/dqc_reference/reference_markers.fasta -out GCF_030159095.1_ASM3015909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:53,578] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:53,581] [INFO] Selected 16 target genomes.
[2024-01-24 14:05:53,582] [INFO] Target genome list was writen to GCF_030159095.1_ASM3015909v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:53,595] [INFO] Task started: fastANI
[2024-01-24 14:05:53,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg95032d8a-0482-401c-8918-60efd1575728/GCF_030159095.1_ASM3015909v1_genomic.fna.gz --refList GCF_030159095.1_ASM3015909v1_genomic.fna/target_genomes.txt --output GCF_030159095.1_ASM3015909v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:13,843] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:13,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2e516c7-42a6-434c-a5ce-44d590094379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:13,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2e516c7-42a6-434c-a5ce-44d590094379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:13,856] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:13,856] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:13,857] [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
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	79.726	1185	1966	95	below_threshold
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	76.7001	234	1966	95	below_threshold
Gemmatimonas phototrophica	strain=AP64	GCA_000695095.2	1379270	1379270	type	True	76.6546	210	1966	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	76.4273	353	1966	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.5669	462	1966	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.5569	472	1966	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.5503	461	1966	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	75.0114	420	1966	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	74.9847	88	1966	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.9429	739	1966	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.94	713	1966	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	74.9197	422	1966	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	74.8775	146	1966	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	74.8744	204	1966	95	below_threshold
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	74.7431	256	1966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:13,858] [INFO] DFAST Taxonomy check result was written to GCF_030159095.1_ASM3015909v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:13,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:13,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:13,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2e516c7-42a6-434c-a5ce-44d590094379/dqc_reference/checkm_data
[2024-01-24 14:06:13,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:13,915] [INFO] Task started: CheckM
[2024-01-24 14:06:13,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030159095.1_ASM3015909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030159095.1_ASM3015909v1_genomic.fna/checkm_input GCF_030159095.1_ASM3015909v1_genomic.fna/checkm_result
[2024-01-24 14:07:37,995] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:37,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:38,016] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:38,016] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:38,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030159095.1_ASM3015909v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:38,017] [INFO] Task started: Blastn
[2024-01-24 14:07:38,017] [INFO] Running command: blastn -query GCF_030159095.1_ASM3015909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2e516c7-42a6-434c-a5ce-44d590094379/dqc_reference/reference_markers_gtdb.fasta -out GCF_030159095.1_ASM3015909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:39,133] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:39,141] [INFO] Selected 22 target genomes.
[2024-01-24 14:07:39,141] [INFO] Target genome list was writen to GCF_030159095.1_ASM3015909v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:39,163] [INFO] Task started: fastANI
[2024-01-24 14:07:39,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg95032d8a-0482-401c-8918-60efd1575728/GCF_030159095.1_ASM3015909v1_genomic.fna.gz --refList GCF_030159095.1_ASM3015909v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030159095.1_ASM3015909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:59,372] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:59,390] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:07:59,391] [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
GCF_000522985.1	s__Gemmatirosa kalamazoonesis	79.7179	1183	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatirosa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361935.1	s__JABFXC01 sp013361935	77.6734	588	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	99.88	99.88	0.94	0.92	3	-
GCA_013361745.1	s__JABFXC01 sp013361745	77.6049	358	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JABFXC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361335.1	s__AG11 sp013361335	77.5355	526	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	99.60	99.48	0.90	0.83	7	-
GCA_016194585.1	s__Fen-1231 sp016194585	77.4584	506	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	99.33	99.33	0.81	0.81	2	-
GCA_011390885.1	s__JAABRT01 sp011390885	77.3075	558	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JAABRT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223455.1	s__AG11 sp003223455	77.2758	536	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813605.1	s__UBA4720 sp013813605	77.2625	125	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__UBA4720	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714015.1	s__PNKF01 sp016714015	77.218	556	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825965.1	s__PNKF01 sp902825965	77.1541	448	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200495.1	s__JACPPC01 sp016200495	77.1446	525	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JACPPC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871855.1	s__PNKL01 sp016871855	77.113	354	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719105.1	s__SCN-70-22 sp016719105	76.9915	537	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	98.70	98.52	0.93	0.89	8	-
GCA_013822425.1	s__PNKL01 sp013822425	76.9184	376	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003171215.1	s__Fen-1231 sp003171215	76.8956	369	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	97.59	95.49	0.88	0.84	3	-
GCA_016741895.1	s__Gemmatimonas sp016741895	76.8556	278	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378185.1	s__AG11 sp014378185	76.8506	200	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__AG11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483225.1	s__Gemmatimonas sp002483225	76.7921	287	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	97.70	97.70	0.96	0.96	2	-
GCA_013822285.1	s__PNKF01 sp013822285	76.7301	220	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876745.1	s__Fen-1231 sp903876745	76.5105	269	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011362545.1	s__DSTP01 sp011362545	76.3137	434	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__DSTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805735.1	s__Longimicrobium sp902805735	75.8476	449	1966	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__Longimicrobiaceae;g__Longimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:59,405] [INFO] GTDB search result was written to GCF_030159095.1_ASM3015909v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:59,406] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:59,411] [INFO] DFAST_QC result json was written to GCF_030159095.1_ASM3015909v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:59,411] [INFO] DFAST_QC completed!
[2024-01-24 14:07:59,411] [INFO] Total running time: 0h2m25s