[2024-01-24 13:31:33,447] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg32fcfaac-c450-42c7-8f5d-7fccf0d9e67d/dqc_reference
[2024-01-24 13:31:34,921] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,922] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,922] [INFO] Running command: gunzip -c /var/lib/cwl/stg08669dbe-1716-4c2d-99ec-d90018bed44b/GCF_021032705.1_ASM2103270v1_genomic.fna.gz | prodigal -d GCF_021032705.1_ASM2103270v1_genomic.fna/cds.fna -a GCF_021032705.1_ASM2103270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:48,597] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:48,597] [INFO] Task started: HMMsearch
[2024-01-24 13:31:48,597] [INFO] Running command: hmmsearch --tblout GCF_021032705.1_ASM2103270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32fcfaac-c450-42c7-8f5d-7fccf0d9e67d/dqc_reference/reference_markers.hmm GCF_021032705.1_ASM2103270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:48,887] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:48,888] [INFO] Found 6/6 markers.
[2024-01-24 13:31:48,932] [INFO] Query marker FASTA was written to GCF_021032705.1_ASM2103270v1_genomic.fna/markers.fasta
[2024-01-24 13:31:48,932] [INFO] Task started: Blastn
[2024-01-24 13:31:48,933] [INFO] Running command: blastn -query GCF_021032705.1_ASM2103270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32fcfaac-c450-42c7-8f5d-7fccf0d9e67d/dqc_reference/reference_markers.fasta -out GCF_021032705.1_ASM2103270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:49,702] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:49,706] [INFO] Selected 20 target genomes.
[2024-01-24 13:31:49,706] [INFO] Target genome list was writen to GCF_021032705.1_ASM2103270v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:49,714] [INFO] Task started: fastANI
[2024-01-24 13:31:49,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg08669dbe-1716-4c2d-99ec-d90018bed44b/GCF_021032705.1_ASM2103270v1_genomic.fna.gz --refList GCF_021032705.1_ASM2103270v1_genomic.fna/target_genomes.txt --output GCF_021032705.1_ASM2103270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:04,582] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:04,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32fcfaac-c450-42c7-8f5d-7fccf0d9e67d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:04,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32fcfaac-c450-42c7-8f5d-7fccf0d9e67d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:04,599] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:04,599] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:04,600] [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
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	100.0	1263	1265	95	conclusive
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	79.1627	491	1265	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	79.0182	479	1265	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	77.9251	265	1265	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	77.7896	224	1265	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	77.778	258	1265	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	77.7092	273	1265	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.6962	231	1265	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	77.6801	296	1265	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	77.6694	280	1265	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	77.5969	272	1265	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.5636	265	1265	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	77.5224	268	1265	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	77.504	227	1265	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	77.4615	209	1265	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	77.4405	280	1265	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.4111	194	1265	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.2009	218	1265	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.1947	214	1265	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.9625	118	1265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:04,602] [INFO] DFAST Taxonomy check result was written to GCF_021032705.1_ASM2103270v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:04,602] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:04,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:04,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32fcfaac-c450-42c7-8f5d-7fccf0d9e67d/dqc_reference/checkm_data
[2024-01-24 13:32:04,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:04,650] [INFO] Task started: CheckM
[2024-01-24 13:32:04,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021032705.1_ASM2103270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021032705.1_ASM2103270v1_genomic.fna/checkm_input GCF_021032705.1_ASM2103270v1_genomic.fna/checkm_result
[2024-01-24 13:32:47,003] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:47,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:47,027] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:47,027] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:47,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021032705.1_ASM2103270v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:47,028] [INFO] Task started: Blastn
[2024-01-24 13:32:47,028] [INFO] Running command: blastn -query GCF_021032705.1_ASM2103270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32fcfaac-c450-42c7-8f5d-7fccf0d9e67d/dqc_reference/reference_markers_gtdb.fasta -out GCF_021032705.1_ASM2103270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:48,080] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:48,083] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:48,084] [INFO] Target genome list was writen to GCF_021032705.1_ASM2103270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:48,095] [INFO] Task started: fastANI
[2024-01-24 13:32:48,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg08669dbe-1716-4c2d-99ec-d90018bed44b/GCF_021032705.1_ASM2103270v1_genomic.fna.gz --refList GCF_021032705.1_ASM2103270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021032705.1_ASM2103270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:58,315] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:58,327] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:32:58,327] [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
GCA_002162685.1	s__Psychroserpens sp002162685	80.1153	663	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014526325.1	s__Psychroserpens algicola	79.9653	655	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	79.3625	617	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104785.1	s__Psychroserpens sp900104785	79.3568	516	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826655.1	s__Psychroserpens damuponensis	79.2247	559	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	79.1721	490	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479815.1	s__Psychroserpens sp905479815	79.0535	521	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826645.1	s__Psychroserpens mesophilus	79.0514	475	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799465.1	s__Psychroserpens sp000799465	78.9171	474	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425305.1	s__Psychroserpens burtonensis	78.7626	536	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
GCA_018222915.1	s__Psychroserpens sp018222915	78.6439	440	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	78.0188	360	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_000828715.1	s__Winogradskyella sp000828715	77.6539	318	1265	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:58,329] [INFO] GTDB search result was written to GCF_021032705.1_ASM2103270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:58,329] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:58,335] [INFO] DFAST_QC result json was written to GCF_021032705.1_ASM2103270v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:58,335] [INFO] DFAST_QC completed!
[2024-01-24 13:32:58,336] [INFO] Total running time: 0h1m25s