[2024-01-24 13:09:34,022] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:34,024] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:34,024] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8e264d6-a67e-493f-995d-b343b44df980/dqc_reference
[2024-01-24 13:09:35,367] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,368] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,368] [INFO] Running command: gunzip -c /var/lib/cwl/stgc48d9894-4124-4f27-b8a7-97bf84adb13f/GCF_000314975.1_ASM31497v1_genomic.fna.gz | prodigal -d GCF_000314975.1_ASM31497v1_genomic.fna/cds.fna -a GCF_000314975.1_ASM31497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:46,517] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:46,517] [INFO] Task started: HMMsearch
[2024-01-24 13:09:46,517] [INFO] Running command: hmmsearch --tblout GCF_000314975.1_ASM31497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8e264d6-a67e-493f-995d-b343b44df980/dqc_reference/reference_markers.hmm GCF_000314975.1_ASM31497v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:46,817] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:46,818] [INFO] Found 6/6 markers.
[2024-01-24 13:09:46,862] [INFO] Query marker FASTA was written to GCF_000314975.1_ASM31497v1_genomic.fna/markers.fasta
[2024-01-24 13:09:46,862] [INFO] Task started: Blastn
[2024-01-24 13:09:46,862] [INFO] Running command: blastn -query GCF_000314975.1_ASM31497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8e264d6-a67e-493f-995d-b343b44df980/dqc_reference/reference_markers.fasta -out GCF_000314975.1_ASM31497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:47,601] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:47,609] [INFO] Selected 25 target genomes.
[2024-01-24 13:09:47,609] [INFO] Target genome list was writen to GCF_000314975.1_ASM31497v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:47,618] [INFO] Task started: fastANI
[2024-01-24 13:09:47,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgc48d9894-4124-4f27-b8a7-97bf84adb13f/GCF_000314975.1_ASM31497v1_genomic.fna.gz --refList GCF_000314975.1_ASM31497v1_genomic.fna/target_genomes.txt --output GCF_000314975.1_ASM31497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:04,094] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:04,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8e264d6-a67e-493f-995d-b343b44df980/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:04,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8e264d6-a67e-493f-995d-b343b44df980/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:04,106] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:04,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:04,107] [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
Aliiglaciecola lipolytica	strain=E3	GCA_000314975.1	477689	477689	type	True	100.0	1571	1575	95	conclusive
Neiella holothuriorum	strain=126	GCA_019457915.1	2870530	2870530	type	True	83.2898	55	1575	95	below_threshold
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	80.0498	108	1575	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	77.7309	104	1575	95	below_threshold
Alteromonas flava	strain=P0211	GCA_002807685.1	2048003	2048003	type	True	77.6195	64	1575	95	below_threshold
Alteromonas facilis	strain=P0213	GCA_002807665.1	2048004	2048004	type	True	77.5249	70	1575	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.5012	110	1575	95	below_threshold
Aestuariibacter halophilus	strain=JC2043	GCA_020687825.1	226011	226011	type	True	77.4281	82	1575	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	77.2251	90	1575	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	77.0586	123	1575	95	below_threshold
Glaciecola pallidula	strain=ACAM 615	GCA_000315035.1	56807	56807	type	True	76.9267	69	1575	95	below_threshold
Paraneptunicella aestuarii	strain=NBU2194	GCA_019900845.1	2831148	2831148	type	True	76.8708	71	1575	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000315075.1	326544	326544	type	True	76.6377	124	1575	95	below_threshold
Catenovulum agarivorans	strain=YM01	GCA_000281085.1	1172192	1172192	type	True	76.4808	53	1575	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:04,108] [INFO] DFAST Taxonomy check result was written to GCF_000314975.1_ASM31497v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:04,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:04,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:04,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8e264d6-a67e-493f-995d-b343b44df980/dqc_reference/checkm_data
[2024-01-24 13:10:04,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:04,156] [INFO] Task started: CheckM
[2024-01-24 13:10:04,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000314975.1_ASM31497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000314975.1_ASM31497v1_genomic.fna/checkm_input GCF_000314975.1_ASM31497v1_genomic.fna/checkm_result
[2024-01-24 13:10:38,790] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:38,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:38,818] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:38,818] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:38,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000314975.1_ASM31497v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:38,819] [INFO] Task started: Blastn
[2024-01-24 13:10:38,819] [INFO] Running command: blastn -query GCF_000314975.1_ASM31497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8e264d6-a67e-493f-995d-b343b44df980/dqc_reference/reference_markers_gtdb.fasta -out GCF_000314975.1_ASM31497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:39,832] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:39,835] [INFO] Selected 19 target genomes.
[2024-01-24 13:10:39,835] [INFO] Target genome list was writen to GCF_000314975.1_ASM31497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:39,896] [INFO] Task started: fastANI
[2024-01-24 13:10:39,896] [INFO] Running command: fastANI --query /var/lib/cwl/stgc48d9894-4124-4f27-b8a7-97bf84adb13f/GCF_000314975.1_ASM31497v1_genomic.fna.gz --refList GCF_000314975.1_ASM31497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000314975.1_ASM31497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:54,011] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:54,025] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:54,026] [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_000314975.1	s__Aliiglaciecola lipolytica	100.0	1571	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliiglaciecola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000315015.1	s__Paraglaciecola mesophila	80.0498	108	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.29	98.05	0.87	0.80	4	-
GCF_018860635.1	s__Aliiglaciecola lipolytica_A	79.9168	609	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliiglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197995.1	s__Aliiglaciecola sp007197995	78.4738	218	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliiglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014225.1	s__Paraglaciecola atlantica_A	77.9694	86	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993955.1	s__Paraglaciecola sp009993955	77.8176	85	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	0.98	0.98	2	-
GCA_000314955.1	s__Paraglaciecola chathamensis	77.7519	116	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.24	97.58	0.90	0.88	8	-
GCF_004360155.1	s__Paraglaciecola sp004360155	77.7309	104	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644725.1	s__Alteromonas sp015644725	77.6233	50	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378905.1	s__Paraglaciecola sp011378905	77.5259	91	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807665.1	s__Alteromonas_E facilis	77.5249	70	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796765.1	s__Paraglaciecola sp009796765	77.3452	111	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906955.1	s__Paraglaciecola mesophila_A	77.3189	110	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506055.1	s__Alteromonas lipotrueae	77.1738	91	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCF_000314995.1	s__Paraglaciecola arctica	77.0586	123	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347635.1	s__Paraglaciecola psychrophila	76.6986	120	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002338515.1	s__Glaciecola sp002338515	76.2782	50	1575	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:54,030] [INFO] GTDB search result was written to GCF_000314975.1_ASM31497v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:54,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:54,036] [INFO] DFAST_QC result json was written to GCF_000314975.1_ASM31497v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:54,036] [INFO] DFAST_QC completed!
[2024-01-24 13:10:54,036] [INFO] Total running time: 0h1m20s