[2023-03-15 05:00:03,422] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:00:03,425] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:00:03,425] [INFO] DQC Reference Directory: /var/lib/cwl/stg82383e28-a108-40ec-94e2-341b2840f75e/dqc_reference
[2023-03-15 05:00:04,514] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:00:04,515] [INFO] Task started: Prodigal
[2023-03-15 05:00:04,515] [INFO] Running command: cat /var/lib/cwl/stg404bcf31-f1fd-47cd-a27d-dcc766872fe6/OceanDNA-b3990.fa | prodigal -d OceanDNA-b3990/cds.fna -a OceanDNA-b3990/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:00:32,711] [INFO] Task succeeded: Prodigal
[2023-03-15 05:00:32,711] [INFO] Task started: HMMsearch
[2023-03-15 05:00:32,711] [INFO] Running command: hmmsearch --tblout OceanDNA-b3990/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82383e28-a108-40ec-94e2-341b2840f75e/dqc_reference/reference_markers.hmm OceanDNA-b3990/protein.faa > /dev/null
[2023-03-15 05:00:32,948] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:00:32,949] [INFO] Found 6/6 markers.
[2023-03-15 05:00:32,984] [INFO] Query marker FASTA was written to OceanDNA-b3990/markers.fasta
[2023-03-15 05:00:32,985] [INFO] Task started: Blastn
[2023-03-15 05:00:32,985] [INFO] Running command: blastn -query OceanDNA-b3990/markers.fasta -db /var/lib/cwl/stg82383e28-a108-40ec-94e2-341b2840f75e/dqc_reference/reference_markers.fasta -out OceanDNA-b3990/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:00:33,532] [INFO] Task succeeded: Blastn
[2023-03-15 05:00:33,536] [INFO] Selected 14 target genomes.
[2023-03-15 05:00:33,537] [INFO] Target genome list was writen to OceanDNA-b3990/target_genomes.txt
[2023-03-15 05:00:33,545] [INFO] Task started: fastANI
[2023-03-15 05:00:33,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg404bcf31-f1fd-47cd-a27d-dcc766872fe6/OceanDNA-b3990.fa --refList OceanDNA-b3990/target_genomes.txt --output OceanDNA-b3990/fastani_result.tsv --threads 1
[2023-03-15 05:00:44,469] [INFO] Task succeeded: fastANI
[2023-03-15 05:00:44,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82383e28-a108-40ec-94e2-341b2840f75e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:00:44,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82383e28-a108-40ec-94e2-341b2840f75e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:00:44,478] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 05:00:44,478] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-15 05:00:44,479] [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
Algoriphagus ornithinivorans	strain=DSM 15282	GCA_900115305.1	226506	226506	type	True	95.9399	1145	1305	95	inconclusive
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	95.124	1165	1305	95	inconclusive
Algoriphagus faecimaris	strain=JCM 16561	GCA_002150585.1	686796	686796	type	True	78.8155	331	1305	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	78.6517	375	1305	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	78.6471	383	1305	95	below_threshold
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	78.4424	307	1305	95	below_threshold
Algoriphagus boseongensis	strain=CECT 8446	GCA_004362805.1	1442587	1442587	type	True	77.7693	266	1305	95	below_threshold
Algoriphagus kandeliae	strain=XY-J91	GCA_004571135.1	2562278	2562278	type	True	77.6878	322	1305	95	below_threshold
Algoriphagus locisalis	strain=DSM 23445	GCA_900116615.1	305507	305507	type	True	77.6869	188	1305	95	below_threshold
Algoriphagus machipongonensis	strain=PR1	GCA_000166275.1	388413	388413	type	True	77.6457	214	1305	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	77.4326	208	1305	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	77.1811	192	1305	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:00:44,502] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3990/tc_result.tsv
[2023-03-15 05:00:44,513] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:00:44,513] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:00:44,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82383e28-a108-40ec-94e2-341b2840f75e/dqc_reference/checkm_data
[2023-03-15 05:00:44,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:00:44,525] [INFO] Task started: CheckM
[2023-03-15 05:00:44,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3990/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3990/checkm_input OceanDNA-b3990/checkm_result
[2023-03-15 05:01:56,039] [INFO] Task succeeded: CheckM
[2023-03-15 05:01:56,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:01:56,061] [INFO] ===== Completeness check finished =====
[2023-03-15 05:01:56,061] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:01:56,061] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3990/markers.fasta)
[2023-03-15 05:01:56,062] [INFO] Task started: Blastn
[2023-03-15 05:01:56,062] [INFO] Running command: blastn -query OceanDNA-b3990/markers.fasta -db /var/lib/cwl/stg82383e28-a108-40ec-94e2-341b2840f75e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3990/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:01:56,830] [INFO] Task succeeded: Blastn
[2023-03-15 05:01:56,836] [INFO] Selected 14 target genomes.
[2023-03-15 05:01:56,837] [INFO] Target genome list was writen to OceanDNA-b3990/target_genomes_gtdb.txt
[2023-03-15 05:01:56,912] [INFO] Task started: fastANI
[2023-03-15 05:01:56,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg404bcf31-f1fd-47cd-a27d-dcc766872fe6/OceanDNA-b3990.fa --refList OceanDNA-b3990/target_genomes_gtdb.txt --output OceanDNA-b3990/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:02:09,494] [INFO] Task succeeded: fastANI
[2023-03-15 05:02:09,503] [INFO] Found 14 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-15 05:02:09,503] [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_900115305.1	s__Algoriphagus ornithinivorans	95.9064	1147	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	95.91	95.63	0.88	0.85	7	inconclusive
GCF_007655305.1	s__Algoriphagus sp007655305	95.1396	1164	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_900101705.1	s__Algoriphagus faecimaris	78.8087	336	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	78.6473	376	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000429465.1	s__Algoriphagus vanfongensis	78.4424	307	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113375.1	s__Algoriphagus hitonicola	77.8398	340	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362805.1	s__Algoriphagus boseongensis	77.7945	264	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807035.1	s__Algoriphagus formosus	77.7808	305	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.55	97.55	0.93	0.93	2	-
GCA_013373335.1	s__Algoriphagus sp013373335	77.7189	221	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116615.1	s__Algoriphagus locisalis	77.6888	188	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571135.1	s__Algoriphagus kandeliae	77.678	323	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166275.1	s__Algoriphagus machipongonensis	77.6458	214	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	77.4326	208	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	77.1811	192	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:02:09,504] [INFO] GTDB search result was written to OceanDNA-b3990/result_gtdb.tsv
[2023-03-15 05:02:09,504] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:02:09,506] [INFO] DFAST_QC result json was written to OceanDNA-b3990/dqc_result.json
[2023-03-15 05:02:09,506] [INFO] DFAST_QC completed!
[2023-03-15 05:02:09,506] [INFO] Total running time: 0h2m6s