[2024-01-25 17:36:05,546] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:36:05,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:36:05,547] [INFO] DQC Reference Directory: /var/lib/cwl/stge1295e67-3d44-460d-b11c-c0d4d506cbcc/dqc_reference
[2024-01-25 17:36:06,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:36:06,668] [INFO] Task started: Prodigal
[2024-01-25 17:36:06,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ecb3b6f-d55d-4402-b07a-93fe7c695f3d/GCF_016906995.1_ASM1690699v1_genomic.fna.gz | prodigal -d GCF_016906995.1_ASM1690699v1_genomic.fna/cds.fna -a GCF_016906995.1_ASM1690699v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:15,777] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:15,777] [INFO] Task started: HMMsearch
[2024-01-25 17:36:15,777] [INFO] Running command: hmmsearch --tblout GCF_016906995.1_ASM1690699v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1295e67-3d44-460d-b11c-c0d4d506cbcc/dqc_reference/reference_markers.hmm GCF_016906995.1_ASM1690699v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:15,988] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:15,989] [INFO] Found 6/6 markers.
[2024-01-25 17:36:16,017] [INFO] Query marker FASTA was written to GCF_016906995.1_ASM1690699v1_genomic.fna/markers.fasta
[2024-01-25 17:36:16,018] [INFO] Task started: Blastn
[2024-01-25 17:36:16,018] [INFO] Running command: blastn -query GCF_016906995.1_ASM1690699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1295e67-3d44-460d-b11c-c0d4d506cbcc/dqc_reference/reference_markers.fasta -out GCF_016906995.1_ASM1690699v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:16,721] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:16,724] [INFO] Selected 29 target genomes.
[2024-01-25 17:36:16,725] [INFO] Target genome list was writen to GCF_016906995.1_ASM1690699v1_genomic.fna/target_genomes.txt
[2024-01-25 17:36:16,732] [INFO] Task started: fastANI
[2024-01-25 17:36:16,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ecb3b6f-d55d-4402-b07a-93fe7c695f3d/GCF_016906995.1_ASM1690699v1_genomic.fna.gz --refList GCF_016906995.1_ASM1690699v1_genomic.fna/target_genomes.txt --output GCF_016906995.1_ASM1690699v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:37,043] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:37,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1295e67-3d44-460d-b11c-c0d4d506cbcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:37,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1295e67-3d44-460d-b11c-c0d4d506cbcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:37,051] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:36:37,051] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:36:37,051] [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
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	79.6843	403	1177	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	78.5711	265	1177	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	78.5422	232	1177	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	78.3606	213	1177	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	78.235	195	1177	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.7153	71	1177	95	below_threshold
Pseudomonas proteolytica	strain=CCUG 51515T	GCA_008692865.1	219574	219574	type	True	76.7072	52	1177	95	below_threshold
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	76.6736	52	1177	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	76.0378	54	1177	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:37,052] [INFO] DFAST Taxonomy check result was written to GCF_016906995.1_ASM1690699v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:37,053] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:37,053] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:37,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1295e67-3d44-460d-b11c-c0d4d506cbcc/dqc_reference/checkm_data
[2024-01-25 17:36:37,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:37,090] [INFO] Task started: CheckM
[2024-01-25 17:36:37,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016906995.1_ASM1690699v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016906995.1_ASM1690699v1_genomic.fna/checkm_input GCF_016906995.1_ASM1690699v1_genomic.fna/checkm_result
[2024-01-25 17:37:06,846] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:06,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:06,882] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:06,882] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:06,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016906995.1_ASM1690699v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:06,882] [INFO] Task started: Blastn
[2024-01-25 17:37:06,882] [INFO] Running command: blastn -query GCF_016906995.1_ASM1690699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1295e67-3d44-460d-b11c-c0d4d506cbcc/dqc_reference/reference_markers_gtdb.fasta -out GCF_016906995.1_ASM1690699v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:08,112] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:08,115] [INFO] Selected 17 target genomes.
[2024-01-25 17:37:08,115] [INFO] Target genome list was writen to GCF_016906995.1_ASM1690699v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:08,125] [INFO] Task started: fastANI
[2024-01-25 17:37:08,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ecb3b6f-d55d-4402-b07a-93fe7c695f3d/GCF_016906995.1_ASM1690699v1_genomic.fna.gz --refList GCF_016906995.1_ASM1690699v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016906995.1_ASM1690699v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:21,043] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:21,056] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:21,056] [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_016906995.1	s__Spongiibacter marinus	100.0	1175	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	97.69	97.65	0.87	0.86	3	conclusive
GCF_000422345.1	s__Spongiibacter marinus_A	94.5988	987	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420325.1	s__Spongiibacter tropicus	79.6843	403	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	-
GCF_012272835.1	s__Spongiibacter sp012272835	78.5865	264	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016132545.1	s__CSC3-9 sp016132545	78.5422	232	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__CSC3-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705705.1	s__KMU-158 sp014705705	78.2274	196	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067195.1	s__Marortus sp018067195	76.8214	142	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	76.7764	62	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_002806685.1	s__Pseudomonas_E qingdaonensis	76.4008	56	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.05	98.91	0.93	0.89	13	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:21,058] [INFO] GTDB search result was written to GCF_016906995.1_ASM1690699v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:21,058] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:21,062] [INFO] DFAST_QC result json was written to GCF_016906995.1_ASM1690699v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:21,062] [INFO] DFAST_QC completed!
[2024-01-25 17:37:21,062] [INFO] Total running time: 0h1m16s