[2024-01-25 18:15:05,401] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:05,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:05,403] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc2035f4-d931-4a1b-8409-e462813202d8/dqc_reference
[2024-01-25 18:15:06,527] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:06,527] [INFO] Task started: Prodigal
[2024-01-25 18:15:06,528] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6b3de77-c92c-47a1-8c61-e3147298d96e/GCF_030010515.1_ASM3001051v1_genomic.fna.gz | prodigal -d GCF_030010515.1_ASM3001051v1_genomic.fna/cds.fna -a GCF_030010515.1_ASM3001051v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:18,382] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:18,382] [INFO] Task started: HMMsearch
[2024-01-25 18:15:18,382] [INFO] Running command: hmmsearch --tblout GCF_030010515.1_ASM3001051v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc2035f4-d931-4a1b-8409-e462813202d8/dqc_reference/reference_markers.hmm GCF_030010515.1_ASM3001051v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:18,642] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:18,643] [INFO] Found 6/6 markers.
[2024-01-25 18:15:18,675] [INFO] Query marker FASTA was written to GCF_030010515.1_ASM3001051v1_genomic.fna/markers.fasta
[2024-01-25 18:15:18,675] [INFO] Task started: Blastn
[2024-01-25 18:15:18,675] [INFO] Running command: blastn -query GCF_030010515.1_ASM3001051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc2035f4-d931-4a1b-8409-e462813202d8/dqc_reference/reference_markers.fasta -out GCF_030010515.1_ASM3001051v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:19,605] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:19,607] [INFO] Selected 22 target genomes.
[2024-01-25 18:15:19,608] [INFO] Target genome list was writen to GCF_030010515.1_ASM3001051v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:19,637] [INFO] Task started: fastANI
[2024-01-25 18:15:19,637] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6b3de77-c92c-47a1-8c61-e3147298d96e/GCF_030010515.1_ASM3001051v1_genomic.fna.gz --refList GCF_030010515.1_ASM3001051v1_genomic.fna/target_genomes.txt --output GCF_030010515.1_ASM3001051v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:37,120] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:37,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc2035f4-d931-4a1b-8409-e462813202d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:37,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc2035f4-d931-4a1b-8409-e462813202d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:37,133] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:15:37,133] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:15:37,134] [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
Cobetia marina	strain=JCM 21022	GCA_001720485.1	28258	28258	type	True	98.6127	1303	1343	95	conclusive
Cobetia crustatorum	strain=JO1	GCA_000591415.1	553385	553385	type	True	83.887	934	1343	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	79.4075	477	1343	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	79.373	453	1343	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	79.0459	457	1343	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	78.8854	448	1343	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	78.8708	407	1343	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.8557	343	1343	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.8191	412	1343	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	78.8133	422	1343	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	78.8036	414	1343	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	78.8003	422	1343	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	78.7562	444	1343	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	78.7081	387	1343	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.671	399	1343	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	78.6646	415	1343	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	78.6254	465	1343	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.5848	388	1343	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.5784	361	1343	95	below_threshold
Halomonas huangheensis	strain=BJGMM-B45	GCA_000470745.1	1178482	1178482	type	True	78.035	299	1343	95	below_threshold
Halomonas cupida	strain=DSM 4740	GCA_900142755.1	44933	44933	type	True	78.0124	344	1343	95	below_threshold
Halomonas huangheensis	strain=BJGMM-B45	GCA_001431725.1	1178482	1178482	type	True	78.0042	301	1343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:37,139] [INFO] DFAST Taxonomy check result was written to GCF_030010515.1_ASM3001051v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:37,140] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:37,140] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:37,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc2035f4-d931-4a1b-8409-e462813202d8/dqc_reference/checkm_data
[2024-01-25 18:15:37,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:37,181] [INFO] Task started: CheckM
[2024-01-25 18:15:37,181] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030010515.1_ASM3001051v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030010515.1_ASM3001051v1_genomic.fna/checkm_input GCF_030010515.1_ASM3001051v1_genomic.fna/checkm_result
[2024-01-25 18:16:26,899] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:26,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:26,919] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:26,919] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:26,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030010515.1_ASM3001051v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:26,920] [INFO] Task started: Blastn
[2024-01-25 18:16:26,920] [INFO] Running command: blastn -query GCF_030010515.1_ASM3001051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc2035f4-d931-4a1b-8409-e462813202d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_030010515.1_ASM3001051v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:28,685] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:28,688] [INFO] Selected 12 target genomes.
[2024-01-25 18:16:28,688] [INFO] Target genome list was writen to GCF_030010515.1_ASM3001051v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:28,700] [INFO] Task started: fastANI
[2024-01-25 18:16:28,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6b3de77-c92c-47a1-8c61-e3147298d96e/GCF_030010515.1_ASM3001051v1_genomic.fna.gz --refList GCF_030010515.1_ASM3001051v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030010515.1_ASM3001051v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:38,596] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:38,604] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:38,604] [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_001720485.1	s__Cobetia marina	98.6127	1303	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	98.51	98.31	0.95	0.93	9	conclusive
GCF_000754225.1	s__Cobetia amphilecti	88.6023	1097	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	96.77	95.09	0.91	0.86	19	-
GCF_000591415.1	s__Cobetia crustatorum	83.887	934	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	98.71	98.71	0.93	0.93	2	-
GCF_009796845.1	s__Cobetia sp009796845	82.8447	1003	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	79.4182	476	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_007989465.1	s__Halomonas halophila	79.3728	454	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCA_001577635.1	s__Halomonas_C sp001577635	79.0989	437	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	79.0799	455	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192275.1	s__Halomonas stenophila	79.056	456	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993675.1	s__Halomonas_C sp010993675	78.9778	426	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117855.1	s__Halomonas_C coralii	78.7537	463	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731955.1	s__Halomonas_C zincidurans	78.6544	416	1343	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:38,606] [INFO] GTDB search result was written to GCF_030010515.1_ASM3001051v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:38,606] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:38,609] [INFO] DFAST_QC result json was written to GCF_030010515.1_ASM3001051v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:38,610] [INFO] DFAST_QC completed!
[2024-01-25 18:16:38,610] [INFO] Total running time: 0h1m33s