[2024-01-24 11:59:10,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:10,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:10,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg01930cf1-efcd-445b-adc0-dd4fd4a4c5e2/dqc_reference
[2024-01-24 11:59:12,228] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:12,229] [INFO] Task started: Prodigal
[2024-01-24 11:59:12,229] [INFO] Running command: gunzip -c /var/lib/cwl/stgf38b1de7-33b7-4d53-a7d4-490ce3ff7486/GCF_004005935.1_ASM400593v1_genomic.fna.gz | prodigal -d GCF_004005935.1_ASM400593v1_genomic.fna/cds.fna -a GCF_004005935.1_ASM400593v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:22,070] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:22,071] [INFO] Task started: HMMsearch
[2024-01-24 11:59:22,071] [INFO] Running command: hmmsearch --tblout GCF_004005935.1_ASM400593v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01930cf1-efcd-445b-adc0-dd4fd4a4c5e2/dqc_reference/reference_markers.hmm GCF_004005935.1_ASM400593v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:22,394] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:22,395] [INFO] Found 6/6 markers.
[2024-01-24 11:59:22,427] [INFO] Query marker FASTA was written to GCF_004005935.1_ASM400593v1_genomic.fna/markers.fasta
[2024-01-24 11:59:22,428] [INFO] Task started: Blastn
[2024-01-24 11:59:22,428] [INFO] Running command: blastn -query GCF_004005935.1_ASM400593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01930cf1-efcd-445b-adc0-dd4fd4a4c5e2/dqc_reference/reference_markers.fasta -out GCF_004005935.1_ASM400593v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:23,100] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:23,103] [INFO] Selected 25 target genomes.
[2024-01-24 11:59:23,103] [INFO] Target genome list was writen to GCF_004005935.1_ASM400593v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:23,112] [INFO] Task started: fastANI
[2024-01-24 11:59:23,112] [INFO] Running command: fastANI --query /var/lib/cwl/stgf38b1de7-33b7-4d53-a7d4-490ce3ff7486/GCF_004005935.1_ASM400593v1_genomic.fna.gz --refList GCF_004005935.1_ASM400593v1_genomic.fna/target_genomes.txt --output GCF_004005935.1_ASM400593v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:39,937] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:39,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01930cf1-efcd-445b-adc0-dd4fd4a4c5e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:39,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01930cf1-efcd-445b-adc0-dd4fd4a4c5e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:39,951] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:39,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:39,951] [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
Neptunomonas marina	strain=HPM-16	GCA_004005935.1	1815562	1815562	type	True	100.0	1211	1213	95	conclusive
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	79.0819	94	1213	95	below_threshold
Neptunomonas concharum	strain=JCM 17730	GCA_006148955.1	1031538	1031538	type	True	78.62	159	1213	95	below_threshold
Neptunomonas antarctica	strain=DSM 22306	GCA_900156635.1	619304	619304	type	True	78.0236	104	1213	95	below_threshold
Neptunomonas qingdaonensis	strain=CGMCC 1.10971	GCA_900113275.1	1045558	1045558	type	True	77.6803	123	1213	95	below_threshold
Neptunomonas qingdaonensis	strain=P10-2-4	GCA_016082375.1	1045558	1045558	type	True	77.6254	122	1213	95	below_threshold
Neptunomonas antarctica	strain=S3-22	GCA_001305295.1	619304	619304	type	True	77.5688	103	1213	95	below_threshold
Neptunomonas japonica	strain=DSM 18939	GCA_000422765.1	417574	417574	type	True	77.5237	126	1213	95	below_threshold
Neptuniibacter caesariensis	strain=MED92	GCA_000153345.1	207954	207954	type	True	77.3875	112	1213	95	below_threshold
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	77.3544	85	1213	95	below_threshold
Nitrincola iocasae	strain=KXZD1103	GCA_008727795.1	2614693	2614693	type	True	77.3434	56	1213	95	below_threshold
Amphritea japonica	strain=JCM 14782	GCA_024347275.1	452627	452627	type	True	77.3232	71	1213	95	below_threshold
Amphritea balenae	strain=JCM 14781	GCA_014646975.1	452629	452629	type	True	77.1745	82	1213	95	below_threshold
Oceanospirillum multiglobuliferum	strain=ATCC 33336	GCA_900167095.1	64969	64969	type	True	76.8725	50	1213	95	below_threshold
Oceanospirillum beijerinckii	strain=DSM 7166	GCA_000422425.1	64976	64976	type	True	76.6979	62	1213	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:39,954] [INFO] DFAST Taxonomy check result was written to GCF_004005935.1_ASM400593v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:39,954] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:39,955] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:39,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01930cf1-efcd-445b-adc0-dd4fd4a4c5e2/dqc_reference/checkm_data
[2024-01-24 11:59:39,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:40,002] [INFO] Task started: CheckM
[2024-01-24 11:59:40,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004005935.1_ASM400593v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004005935.1_ASM400593v1_genomic.fna/checkm_input GCF_004005935.1_ASM400593v1_genomic.fna/checkm_result
[2024-01-24 12:00:14,001] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:14,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:14,023] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:14,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:14,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004005935.1_ASM400593v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:14,024] [INFO] Task started: Blastn
[2024-01-24 12:00:14,024] [INFO] Running command: blastn -query GCF_004005935.1_ASM400593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01930cf1-efcd-445b-adc0-dd4fd4a4c5e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_004005935.1_ASM400593v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:14,858] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:14,861] [INFO] Selected 21 target genomes.
[2024-01-24 12:00:14,861] [INFO] Target genome list was writen to GCF_004005935.1_ASM400593v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:14,876] [INFO] Task started: fastANI
[2024-01-24 12:00:14,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgf38b1de7-33b7-4d53-a7d4-490ce3ff7486/GCF_004005935.1_ASM400593v1_genomic.fna.gz --refList GCF_004005935.1_ASM400593v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004005935.1_ASM400593v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:29,378] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:29,392] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:29,392] [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_004005935.1	s__Neptunomonas marina	100.0	1211	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	97.03	97.03	0.93	0.93	2	conclusive
GCF_018860855.1	s__Amphritea atlantica_A	79.0734	103	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630635.1	s__Neptunomonas concharum	78.6861	157	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	0.98	0.98	2	-
GCF_016592555.1	s__Neptunomonas japonica_A	77.7437	128	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113275.1	s__Neptunomonas qingdaonensis	77.7061	122	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001305295.1	s__Neptunomonas antarctica	77.6117	103	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000422765.1	s__Neptunomonas japonica	77.5294	125	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223185.1	s__Amphritea sp018223185	77.5265	65	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.96	99.96	0.97	0.97	2	-
GCA_016744175.1	s__Neptunomonas sp016744175	77.5126	128	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptunomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209595.1	s__Pontibacterium sp015209595	77.4308	111	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Pontibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153345.1	s__Neptuniibacter caesariensis	77.4131	111	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858655.1	s__Amphritea balenae	77.3544	85	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018067325.1	s__Amphritea sp018067325	76.9255	58	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.51	99.51	0.92	0.92	2	-
GCF_004339595.1	s__Marinobacterium mangrovicola	76.8131	71	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422425.1	s__Oceanospirillum beijerinckii	76.6868	62	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	98.77	98.77	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:29,394] [INFO] GTDB search result was written to GCF_004005935.1_ASM400593v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:29,395] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:29,398] [INFO] DFAST_QC result json was written to GCF_004005935.1_ASM400593v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:29,399] [INFO] DFAST_QC completed!
[2024-01-24 12:00:29,399] [INFO] Total running time: 0h1m18s