[2024-01-24 10:57:35,515] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:35,517] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:35,517] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5f47a54-9597-4427-a58a-afb9fd12e902/dqc_reference
[2024-01-24 10:57:36,710] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:36,711] [INFO] Task started: Prodigal
[2024-01-24 10:57:36,711] [INFO] Running command: gunzip -c /var/lib/cwl/stg07016d71-4e2f-4f8e-9947-9abd3d619957/GCF_003987265.1_ASM398726v1_genomic.fna.gz | prodigal -d GCF_003987265.1_ASM398726v1_genomic.fna/cds.fna -a GCF_003987265.1_ASM398726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:44,393] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:44,394] [INFO] Task started: HMMsearch
[2024-01-24 10:57:44,394] [INFO] Running command: hmmsearch --tblout GCF_003987265.1_ASM398726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5f47a54-9597-4427-a58a-afb9fd12e902/dqc_reference/reference_markers.hmm GCF_003987265.1_ASM398726v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:44,645] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:44,647] [INFO] Found 6/6 markers.
[2024-01-24 10:57:44,688] [INFO] Query marker FASTA was written to GCF_003987265.1_ASM398726v1_genomic.fna/markers.fasta
[2024-01-24 10:57:44,689] [INFO] Task started: Blastn
[2024-01-24 10:57:44,689] [INFO] Running command: blastn -query GCF_003987265.1_ASM398726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5f47a54-9597-4427-a58a-afb9fd12e902/dqc_reference/reference_markers.fasta -out GCF_003987265.1_ASM398726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:45,463] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:45,466] [INFO] Selected 17 target genomes.
[2024-01-24 10:57:45,466] [INFO] Target genome list was writen to GCF_003987265.1_ASM398726v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:45,555] [INFO] Task started: fastANI
[2024-01-24 10:57:45,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg07016d71-4e2f-4f8e-9947-9abd3d619957/GCF_003987265.1_ASM398726v1_genomic.fna.gz --refList GCF_003987265.1_ASM398726v1_genomic.fna/target_genomes.txt --output GCF_003987265.1_ASM398726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:54,403] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:54,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5f47a54-9597-4427-a58a-afb9fd12e902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:54,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5f47a54-9597-4427-a58a-afb9fd12e902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:54,414] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:54,414] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:54,415] [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
Pseudidiomarina sediminum	strain=c121	GCA_003987265.1	431675	431675	type	True	100.0	869	871	95	conclusive
Pseudidiomarina sediminum	strain=DSM 21906	GCA_000423165.1	431675	431675	type	True	99.9921	869	871	95	conclusive
Pseudidiomarina aquimaris	strain=SW15	GCA_003987395.1	641841	641841	type	True	79.4569	324	871	95	below_threshold
Pseudidiomarina homiensis	strain=PO-M2	GCA_003987225.1	364198	364198	type	True	79.2438	297	871	95	below_threshold
Pseudidiomarina piscicola	strain=CECT 9734	GCA_902806985.1	2614830	2614830	type	True	79.1563	260	871	95	below_threshold
Pseudidiomarina insulisalsae	strain=CVS-6	GCA_003987065.1	575789	575789	type	True	79.1226	301	871	95	below_threshold
Pseudidiomarina halophila	strain=BH195	GCA_003987215.1	1449799	1449799	type	True	79.0324	265	871	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	78.8007	199	871	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	78.776	200	871	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	78.6999	186	871	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	78.6257	200	871	95	below_threshold
Pseudidiomarina planktonica	strain=CGMCC 1.12458	GCA_900177775.1	1323738	1323738	type	True	78.0564	131	871	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	77.2194	68	871	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:54,416] [INFO] DFAST Taxonomy check result was written to GCF_003987265.1_ASM398726v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:54,417] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:54,417] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:54,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5f47a54-9597-4427-a58a-afb9fd12e902/dqc_reference/checkm_data
[2024-01-24 10:57:54,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:54,445] [INFO] Task started: CheckM
[2024-01-24 10:57:54,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987265.1_ASM398726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987265.1_ASM398726v1_genomic.fna/checkm_input GCF_003987265.1_ASM398726v1_genomic.fna/checkm_result
[2024-01-24 10:58:22,806] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:22,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:22,826] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:22,826] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:22,827] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987265.1_ASM398726v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:22,827] [INFO] Task started: Blastn
[2024-01-24 10:58:22,827] [INFO] Running command: blastn -query GCF_003987265.1_ASM398726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5f47a54-9597-4427-a58a-afb9fd12e902/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987265.1_ASM398726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:24,047] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:24,052] [INFO] Selected 15 target genomes.
[2024-01-24 10:58:24,052] [INFO] Target genome list was writen to GCF_003987265.1_ASM398726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:24,065] [INFO] Task started: fastANI
[2024-01-24 10:58:24,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg07016d71-4e2f-4f8e-9947-9abd3d619957/GCF_003987265.1_ASM398726v1_genomic.fna.gz --refList GCF_003987265.1_ASM398726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987265.1_ASM398726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:31,770] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:31,790] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:31,791] [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_000423165.1	s__Pseudidiomarina sediminum	99.9921	869	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003987395.1	s__Pseudidiomarina aquimaris	79.4644	323	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.26	97.14	0.86	0.77	3	-
GCF_003987225.1	s__Pseudidiomarina homiensis	79.2259	299	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902806985.1	s__Pseudidiomarina piscicola	79.1563	260	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987065.1	s__Pseudidiomarina insulisalsae	79.1157	302	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987215.1	s__Pseudidiomarina halophila	79.05	264	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	78.9689	201	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003030745.1	s__Pseudidiomarina aestuarii_A	78.8652	73	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	78.7674	201	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000753735.1	s__Pseudidiomarina atlantica	78.7264	285	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279005.1	s__Pseudidiomarina sp002279005	78.6506	164	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	78.6182	199	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_900177775.1	s__Pseudidiomarina planktonica	78.0564	131	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003999375.1	s__Pseudidiomarina mangrovi	77.9816	161	871	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:31,793] [INFO] GTDB search result was written to GCF_003987265.1_ASM398726v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:31,794] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:31,798] [INFO] DFAST_QC result json was written to GCF_003987265.1_ASM398726v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:31,798] [INFO] DFAST_QC completed!
[2024-01-24 10:58:31,798] [INFO] Total running time: 0h0m56s