[2023-06-30 22:22:20,042] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:22:20,058] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:22:20,058] [INFO] DQC Reference Directory: /var/lib/cwl/stgdca89c93-de84-4429-93d5-c5ba7813eb55/dqc_reference
[2023-06-30 22:22:21,660] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:22:21,661] [INFO] Task started: Prodigal
[2023-06-30 22:22:21,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg5562f6b0-6322-474d-83f7-50a3a65dda5d/GCA_019746785.1_ASM1974678v1_genomic.fna.gz | prodigal -d GCA_019746785.1_ASM1974678v1_genomic.fna/cds.fna -a GCA_019746785.1_ASM1974678v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:22:27,268] [INFO] Task succeeded: Prodigal
[2023-06-30 22:22:27,268] [INFO] Task started: HMMsearch
[2023-06-30 22:22:27,268] [INFO] Running command: hmmsearch --tblout GCA_019746785.1_ASM1974678v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdca89c93-de84-4429-93d5-c5ba7813eb55/dqc_reference/reference_markers.hmm GCA_019746785.1_ASM1974678v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:22:27,478] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:22:27,480] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5562f6b0-6322-474d-83f7-50a3a65dda5d/GCA_019746785.1_ASM1974678v1_genomic.fna.gz]
[2023-06-30 22:22:27,510] [INFO] Query marker FASTA was written to GCA_019746785.1_ASM1974678v1_genomic.fna/markers.fasta
[2023-06-30 22:22:27,511] [INFO] Task started: Blastn
[2023-06-30 22:22:27,511] [INFO] Running command: blastn -query GCA_019746785.1_ASM1974678v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdca89c93-de84-4429-93d5-c5ba7813eb55/dqc_reference/reference_markers.fasta -out GCA_019746785.1_ASM1974678v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:22:28,394] [INFO] Task succeeded: Blastn
[2023-06-30 22:22:28,398] [INFO] Selected 16 target genomes.
[2023-06-30 22:22:28,398] [INFO] Target genome list was writen to GCA_019746785.1_ASM1974678v1_genomic.fna/target_genomes.txt
[2023-06-30 22:22:28,399] [INFO] Task started: fastANI
[2023-06-30 22:22:28,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg5562f6b0-6322-474d-83f7-50a3a65dda5d/GCA_019746785.1_ASM1974678v1_genomic.fna.gz --refList GCA_019746785.1_ASM1974678v1_genomic.fna/target_genomes.txt --output GCA_019746785.1_ASM1974678v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:22:39,669] [INFO] Task succeeded: fastANI
[2023-06-30 22:22:39,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdca89c93-de84-4429-93d5-c5ba7813eb55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:22:39,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdca89c93-de84-4429-93d5-c5ba7813eb55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:22:39,684] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:22:39,684] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 22:22:39,684] [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
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	81.1601	93	178	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	80.6507	102	178	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	80.412	92	178	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	80.3173	105	178	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	80.0991	80	178	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	79.8849	81	178	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	79.4224	94	178	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	79.3664	77	178	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 22:22:39,688] [INFO] DFAST Taxonomy check result was written to GCA_019746785.1_ASM1974678v1_genomic.fna/tc_result.tsv
[2023-06-30 22:22:39,689] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:22:39,689] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:22:39,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdca89c93-de84-4429-93d5-c5ba7813eb55/dqc_reference/checkm_data
[2023-06-30 22:22:39,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:22:39,721] [INFO] Task started: CheckM
[2023-06-30 22:22:39,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019746785.1_ASM1974678v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019746785.1_ASM1974678v1_genomic.fna/checkm_input GCA_019746785.1_ASM1974678v1_genomic.fna/checkm_result
[2023-06-30 22:23:02,753] [INFO] Task succeeded: CheckM
[2023-06-30 22:23:02,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 22:23:02,774] [INFO] ===== Completeness check finished =====
[2023-06-30 22:23:02,775] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:23:02,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019746785.1_ASM1974678v1_genomic.fna/markers.fasta)
[2023-06-30 22:23:02,776] [INFO] Task started: Blastn
[2023-06-30 22:23:02,776] [INFO] Running command: blastn -query GCA_019746785.1_ASM1974678v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdca89c93-de84-4429-93d5-c5ba7813eb55/dqc_reference/reference_markers_gtdb.fasta -out GCA_019746785.1_ASM1974678v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:23:04,118] [INFO] Task succeeded: Blastn
[2023-06-30 22:23:04,122] [INFO] Selected 20 target genomes.
[2023-06-30 22:23:04,122] [INFO] Target genome list was writen to GCA_019746785.1_ASM1974678v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:23:04,167] [INFO] Task started: fastANI
[2023-06-30 22:23:04,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg5562f6b0-6322-474d-83f7-50a3a65dda5d/GCA_019746785.1_ASM1974678v1_genomic.fna.gz --refList GCA_019746785.1_ASM1974678v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019746785.1_ASM1974678v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:23:17,711] [INFO] Task succeeded: fastANI
[2023-06-30 22:23:17,725] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 22:23:17,726] [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_014380005.1	s__Magnetospirillum sp014380005	85.1629	129	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379805.1	s__Magnetospirillum sp014379805	82.8532	109	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011022235.1	s__Magnetospirillum aberrantis	81.1601	93	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650635.1	s__Magnetospirillum moscoviense	80.4745	91	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCA_001898825.1	s__Magnetospirillum sp001898825	80.3807	90	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	95.98	95.98	0.88	0.88	2	-
GCF_000513295.1	s__Magnetospirillum gryphiswaldense	80.3173	105	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	97.87	97.87	0.91	0.91	3	-
GCF_900184795.1	s__Phaeospirillum sp900184795	80.141	86	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650715.1	s__Phaeospirillum marisnigri	80.0991	80	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941095.1	s__Magnetospirillum sp903941095	80.014	86	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.83	99.83	0.93	0.93	2	-
GCF_902729435.1	s__Magnetospirillum sp902729435	79.8322	101	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224925.1	s__Magnetospirillum sp018224925	79.6226	94	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342045.1	s__Phaeospirillum caucaseum	79.4224	94	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284725.1	s__Phaeospirillum kuznetsovii	79.3664	77	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105535.1	s__Phaeospirillum sp002105535	79.3324	91	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	79.1573	84	178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 22:23:17,727] [INFO] GTDB search result was written to GCA_019746785.1_ASM1974678v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:23:17,728] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:23:17,732] [INFO] DFAST_QC result json was written to GCA_019746785.1_ASM1974678v1_genomic.fna/dqc_result.json
[2023-06-30 22:23:17,732] [INFO] DFAST_QC completed!
[2023-06-30 22:23:17,732] [INFO] Total running time: 0h0m58s