[2024-01-24 13:52:12,596] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:52:12,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:52:12,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg5796bf36-a547-4a83-862e-e713c5d1f83e/dqc_reference
[2024-01-24 13:52:13,788] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:52:13,789] [INFO] Task started: Prodigal
[2024-01-24 13:52:13,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg053910bd-74d4-4e0b-b5ae-84d949009db2/GCF_003987355.1_ASM398735v1_genomic.fna.gz | prodigal -d GCF_003987355.1_ASM398735v1_genomic.fna/cds.fna -a GCF_003987355.1_ASM398735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:52:21,175] [INFO] Task succeeded: Prodigal
[2024-01-24 13:52:21,176] [INFO] Task started: HMMsearch
[2024-01-24 13:52:21,176] [INFO] Running command: hmmsearch --tblout GCF_003987355.1_ASM398735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5796bf36-a547-4a83-862e-e713c5d1f83e/dqc_reference/reference_markers.hmm GCF_003987355.1_ASM398735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:52:21,435] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:52:21,437] [INFO] Found 6/6 markers.
[2024-01-24 13:52:21,465] [INFO] Query marker FASTA was written to GCF_003987355.1_ASM398735v1_genomic.fna/markers.fasta
[2024-01-24 13:52:21,465] [INFO] Task started: Blastn
[2024-01-24 13:52:21,465] [INFO] Running command: blastn -query GCF_003987355.1_ASM398735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5796bf36-a547-4a83-862e-e713c5d1f83e/dqc_reference/reference_markers.fasta -out GCF_003987355.1_ASM398735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:22,189] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:22,192] [INFO] Selected 24 target genomes.
[2024-01-24 13:52:22,193] [INFO] Target genome list was writen to GCF_003987355.1_ASM398735v1_genomic.fna/target_genomes.txt
[2024-01-24 13:52:22,208] [INFO] Task started: fastANI
[2024-01-24 13:52:22,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg053910bd-74d4-4e0b-b5ae-84d949009db2/GCF_003987355.1_ASM398735v1_genomic.fna.gz --refList GCF_003987355.1_ASM398735v1_genomic.fna/target_genomes.txt --output GCF_003987355.1_ASM398735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:35,039] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:35,040] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5796bf36-a547-4a83-862e-e713c5d1f83e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:35,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5796bf36-a547-4a83-862e-e713c5d1f83e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:35,054] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:52:35,054] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:35,054] [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 aestuarii	strain=KYW314	GCA_003987355.1	624146	624146	suspected-type	True	100.0	875	875	95	conclusive
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	78.7895	168	875	95	below_threshold
Pseudidiomarina gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	78.738	165	875	95	below_threshold
Pseudidiomarina homiensis	strain=PO-M2	GCA_003987225.1	364198	364198	type	True	78.718	159	875	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	78.5702	179	875	95	below_threshold
Pseudidiomarina piscicola	strain=CECT 9734	GCA_902806985.1	2614830	2614830	type	True	78.48	137	875	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	78.46	159	875	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	78.4503	174	875	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	78.4347	160	875	95	below_threshold
Pseudidiomarina atlantica	strain=MCCC 1A10513	GCA_000753735.1	1517416	1517416	type	True	78.2304	157	875	95	below_threshold
Idiomarina xiamenensis	strain=10-D-4	GCA_000299895.1	1207041	1207041	type	True	77.8291	74	875	95	below_threshold
Idiomarina ramblicola	strain=R22	GCA_003987255.1	263724	263724	type	True	77.8	60	875	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	77.7216	68	875	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	77.3075	68	875	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:35,056] [INFO] DFAST Taxonomy check result was written to GCF_003987355.1_ASM398735v1_genomic.fna/tc_result.tsv
[2024-01-24 13:52:35,057] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:35,057] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:35,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5796bf36-a547-4a83-862e-e713c5d1f83e/dqc_reference/checkm_data
[2024-01-24 13:52:35,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:35,089] [INFO] Task started: CheckM
[2024-01-24 13:52:35,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987355.1_ASM398735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987355.1_ASM398735v1_genomic.fna/checkm_input GCF_003987355.1_ASM398735v1_genomic.fna/checkm_result
[2024-01-24 13:53:02,509] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:02,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:02,531] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:02,531] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:02,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987355.1_ASM398735v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:02,532] [INFO] Task started: Blastn
[2024-01-24 13:53:02,532] [INFO] Running command: blastn -query GCF_003987355.1_ASM398735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5796bf36-a547-4a83-862e-e713c5d1f83e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987355.1_ASM398735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:03,601] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:03,606] [INFO] Selected 18 target genomes.
[2024-01-24 13:53:03,606] [INFO] Target genome list was writen to GCF_003987355.1_ASM398735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:03,621] [INFO] Task started: fastANI
[2024-01-24 13:53:03,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg053910bd-74d4-4e0b-b5ae-84d949009db2/GCF_003987355.1_ASM398735v1_genomic.fna.gz --refList GCF_003987355.1_ASM398735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987355.1_ASM398735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:12,517] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:12,533] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:53:12,534] [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_003987355.1	s__Pseudidiomarina aestuarii	100.0	875	875	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003030745.1	s__Pseudidiomarina aestuarii_A	88.3675	331	875	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987045.1	s__Pseudidiomarina marina	78.7273	171	875	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCF_004025325.1	s__Pseudidiomarina gelatinasegens	78.7264	165	875	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	78.6264	147	875	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753715.1	s__Pseudidiomarina salinarum	78.6239	121	875	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	78.5792	178	875	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	78.5095	136	875	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	78.4716	173	875	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001418345.1	s__Pseudidiomarina woesei	78.4516	160	875	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000753735.1	s__Pseudidiomarina atlantica	78.2304	157	875	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	77.9676	169	875	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999375.1	s__Pseudidiomarina mangrovi	77.8311	164	875	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299895.1	s__Idiomarina xiamenensis	77.8291	74	875	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:12,535] [INFO] GTDB search result was written to GCF_003987355.1_ASM398735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:12,536] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:12,540] [INFO] DFAST_QC result json was written to GCF_003987355.1_ASM398735v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:12,540] [INFO] DFAST_QC completed!
[2024-01-24 13:53:12,540] [INFO] Total running time: 0h0m60s