[2024-01-24 13:03:20,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:03:20,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:03:20,816] [INFO] DQC Reference Directory: /var/lib/cwl/stged72b0e1-5254-4bd1-bda0-ef74703f33b1/dqc_reference
[2024-01-24 13:03:22,040] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:03:22,041] [INFO] Task started: Prodigal
[2024-01-24 13:03:22,041] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5eb8d87-6279-4c97-a4b4-4d832d5ca998/GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna.gz | prodigal -d GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/cds.fna -a GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:03:40,639] [INFO] Task succeeded: Prodigal
[2024-01-24 13:03:40,639] [INFO] Task started: HMMsearch
[2024-01-24 13:03:40,639] [INFO] Running command: hmmsearch --tblout GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged72b0e1-5254-4bd1-bda0-ef74703f33b1/dqc_reference/reference_markers.hmm GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:03:40,974] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:03:40,975] [INFO] Found 6/6 markers.
[2024-01-24 13:03:41,034] [INFO] Query marker FASTA was written to GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/markers.fasta
[2024-01-24 13:03:41,035] [INFO] Task started: Blastn
[2024-01-24 13:03:41,035] [INFO] Running command: blastn -query GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/markers.fasta -db /var/lib/cwl/stged72b0e1-5254-4bd1-bda0-ef74703f33b1/dqc_reference/reference_markers.fasta -out GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:41,721] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:41,724] [INFO] Selected 13 target genomes.
[2024-01-24 13:03:41,724] [INFO] Target genome list was writen to GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/target_genomes.txt
[2024-01-24 13:03:41,730] [INFO] Task started: fastANI
[2024-01-24 13:03:41,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5eb8d87-6279-4c97-a4b4-4d832d5ca998/GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna.gz --refList GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/target_genomes.txt --output GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:03:54,364] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:54,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged72b0e1-5254-4bd1-bda0-ef74703f33b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:03:54,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged72b0e1-5254-4bd1-bda0-ef74703f33b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:03:54,383] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:03:54,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:03:54,383] [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
Aquimarina macrocephali	strain=JAMB N27	GCA_000520995.1	666563	666563	type	True	100.0	1958	1961	95	conclusive
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	89.5098	1531	1961	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	88.451	1496	1961	95	below_threshold
Aquimarina sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	80.301	935	1961	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	80.0368	825	1961	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	80.0118	863	1961	95	below_threshold
Aquimarina mytili	strain=KCTC 23302	GCA_016735115.1	874423	874423	type	True	79.2289	620	1961	95	below_threshold
Aquimarina spongiae	strain=DSM 22623	GCA_900141785.1	570521	570521	type	True	78.3188	490	1961	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	76.6031	70	1961	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.5182	101	1961	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.476	103	1961	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	75.897	122	1961	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	75.6036	124	1961	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:03:54,386] [INFO] DFAST Taxonomy check result was written to GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/tc_result.tsv
[2024-01-24 13:03:54,387] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:03:54,387] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:03:54,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged72b0e1-5254-4bd1-bda0-ef74703f33b1/dqc_reference/checkm_data
[2024-01-24 13:03:54,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:03:54,505] [INFO] Task started: CheckM
[2024-01-24 13:03:54,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/checkm_input GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/checkm_result
[2024-01-24 13:04:49,258] [INFO] Task succeeded: CheckM
[2024-01-24 13:04:49,260] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:04:49,285] [INFO] ===== Completeness check finished =====
[2024-01-24 13:04:49,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:04:49,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/markers.fasta)
[2024-01-24 13:04:49,286] [INFO] Task started: Blastn
[2024-01-24 13:04:49,287] [INFO] Running command: blastn -query GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/markers.fasta -db /var/lib/cwl/stged72b0e1-5254-4bd1-bda0-ef74703f33b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:50,149] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:50,153] [INFO] Selected 6 target genomes.
[2024-01-24 13:04:50,153] [INFO] Target genome list was writen to GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:50,159] [INFO] Task started: fastANI
[2024-01-24 13:04:50,160] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5eb8d87-6279-4c97-a4b4-4d832d5ca998/GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna.gz --refList GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/target_genomes_gtdb.txt --output GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:59,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:59,149] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:04:59,149] [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_000520995.1	s__Aquimarina macrocephali	100.0	1958	1961	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900299525.1	s__Aquimarina sp900299525	94.9461	1637	1961	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900312745.1	s__Aquimarina sp900312745	90.1588	1573	1961	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.61	95.54	0.91	0.91	4	-
GCF_000520975.1	s__Aquimarina megaterium	89.5168	1530	1961	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.79	98.77	0.92	0.92	4	-
GCF_002846555.1	s__Aquimarina sp002846555	89.4609	1400	1961	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000626715.1	s__Aquimarina atlantica	88.4559	1495	1961	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:04:59,151] [INFO] GTDB search result was written to GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:59,151] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:59,154] [INFO] DFAST_QC result json was written to GCF_000520995.1_of_Aquimarina_macrocephali_genomic.fna/dqc_result.json
[2024-01-24 13:04:59,155] [INFO] DFAST_QC completed!
[2024-01-24 13:04:59,155] [INFO] Total running time: 0h1m38s